Indigenous Puerto Rico: DNA evidence upsets established history

iStock / Large sculpture of Taino Indian in Isabela, Puerto Rico.

Rick Kearns

A blending of Taino, Spanish and African in DNA evidence.

History is written by the conquerors. The Native peoples of North America know this all too well, as they are still trying to bring the truth to light. Now, their long-lost Caribbean cousins are beginning the same process.

It’s an uphill battle.

Most Puerto Ricans know, or think they know, their ethnic and racial history: a blending of Taino (Indian), Spanish and African. Students of the islands’ past have read the same account for over 300 years; that the Native people, and their societies, were killed off by the Spanish invaders by the 1600s. It was always noted though, how many of the original colonists married Taino women or had Taino concubines, producing the original mestizaje (mixture) that, when blended with African, would produce Puerto Ricans.

Those first unions, according to the conventional wisdom, explain why some Puerto Ricans have “a little bit” of Native heritage. Mainly we are Spanish, we are told, with a little African blood and far-away Taino ancestry.

But the order of that sequence will have to change.

Dr. Juan Martinez-Cruzado, a geneticist from the University of Puerto Rico Mayaguez who designed an island-wide DNA survey, released the final numbers and analysis of the project in 2003, and these results tell a different story.

According to the study funded by the U.S. National Science Foundation, 61 percent of all Puerto Ricans have Amerindian mitochondrial DNA, 27 percent have African and 12 percent Caucasian. (Nuclear DNA, or the genetic material present in a gene’s nucleus, is inherited in equal parts from one’s father and mother. Mitochondrial DNA is inherited only from one’s mother and does not change or blend with other materials over time.)

In other words a majority of Puerto Ricans have Native blood.

“Our study showed there was assimilation,” Martinez-Cruzado explained, “but the people were not extinguished. Their political and social structure was but the genes were not.

“The people were assimilated into a new colonial order and became mixed – but that’s what Puerto Ricans are: Indians mixed with Africans and Spaniards,” he asserted.

“There has been an under-estimation of the Amerindian heritage of Puerto Rico, much larger than most historians will admit,” he said.

Martinez-Cruzado cited the historical descriptions of life in Puerto Rico during the 17th and 18th centuries as an example.

“These accounts describe many aspects that are totally derived from Taino modus vivendi, not just the hammocks but the way they fished, their methods of farming, etc.,” he related. “It is clear that the influence of Taino culture was very strong up to about 200 years ago. If we could conduct this same study on the Puerto Ricans from those times, the figure would show that 80 percent of the people had Indian heritage.”

Another historical moment that should receive more attention involves the story of a group of Tainos who, after 200 years of absence from official head-counts, appeared in a military census from the 1790s. In this episode, a colonial military census noted that all of a sudden there were 2,000 Indians living in a northwestern mountain region. “These were Indians who the Spanish had placed on the tiny island of Mona (just off the western coast of Puerto Rico) who survived in isolation and then were brought over,” Martinez-Cruzado said. “They became mixed but there were many Indians who survived but eventually mixed with the Africans and Spaniards. These Mona Tainos must have had a further influence as well.”

Martinez-Cruzado noted how many customs and history were handed down through oral tradition. To this day on the island, there are many people who use medicinal plants and farming methods that come directly from the Tainos.

This is especially true of the areas once known as Indieras, or Indian Zones.

He also pointed out that most of these Native traditions probably do come from the Tainos, the Native people who appeared on the island circa 700 AD. But there were other waves of migrations to Puerto Rico and the entire Caribbean area.

Through the extensive study of the Puerto Rican samples, Martinez-Cruzado and his team have found connections between island residents and Native peoples who arrived before and after the Tainos. He pointed out how a few of the samples can be traced back 9,000 years from ancient migrations, while others correspond to the genetic makeup of Native peoples of the Yucatan, Hispaniola, Margarita Island and Brazil among others. These latter genetic trails point to the presence of other Native peoples who were probably brought to the island as slaves from other Spanish or Portuguese colonies after the 1600s.

While island scholars will have much work to do to catch up with these “new” facts, the genetic detective work for Cruzado is also far from finished. As word spread of the remarkable survey, other scholars from the Dominican Republic, Cuba and Venezuela invited the Puerto Rican scientist to present his findings. They asked him to assist in similar projects in their respective countries.

In 2005, Martinez-Cruzado along with others released Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis.

While Martinez-Cruzado and his colleagues focused on the history of Pre-Columbian migrations, people in the current Taino restoration movement (such as Nacion Taina, The Jatibonicu Taino Tribal Nation of Boriken, Taino Timucua Tribal Council, the United Confederation of Taino People, and others) hoped that many of their compatriots reflected on the following quote: “The DNA story shows that the official story was wrong,” Martinez-Cruzado said. “This means a much larger Amerindian inheritance for Puerto Ricans.”

This story was originally published October 6, 2003.

Comments (17)
No. 1-9

Donde esta el informe oficial?

Donde esta los documentos oficiales que enseñen como fue que se hizo este análisis Y cuantas personas dieron pruebas de dna y donde se hizo y como se escojieron sobre todo como se llego a la conclusión que eso representa a todos los Puertorriqueños como indica el reportaje ya que usa la palabra todos los Puertorriqueños tienen tanto %.

Supuestamente se hicieron 2 diferentes estudios pero no se presenta las pruebas ni el informe. Por que? Eso solo se hace si es una agenda! Si en realidad el motivo es de enseñar entoces se eseña todo como se debe de lo contrario termina sido solo palabras sin sentido ya que le tiene que dar sentido no se puso.

Att: Roland Ramos

Zoe Muntaner
Zoe Muntaner

Take a look here. This might help your questions.


Where did you get these results? I’m sure they are inaccurate. My ancestry results reflect otherwise. We are mainly Spaniards from Southern Spain or the canaries and most of us look it too. This is just more black legend about the Spaniards. We are the descendants of Spanish settlers and conquistadors. We were a province of Spain and with Spain for over 400 years. We are Spanish. Look at the people of places like Nicaragua or Honduras. They are more indigenous and we look nothing like them.


Dumbest, most intellectually dishonest article. It gives no new information, and misleads the reader.

Yes, most boricuas have Taino heritage...and it's usually 15% and under, and this is a fact. I have only ever seen the ancestry results of two boricuas with more than 15% Taino, the rest were under, including myself and my relatives. Boricuas are overwhelmingly Spanish and/or African with SOME DEGREE of Taino, not the other way around.


I can't believe you would rather associate with the Spanish conquerors who raped and pillage our lands and enslaved our people. I for one would rather be called native american.

Marialuisa Garcia
Marialuisa Garcia

I found this article quite interesting in assisting me in understanding my Puerto Rican roots. My mother was not one to discuss my lineage, so I bought the Ancestry DNA kit. I was shocked when it revealed that I was 24% Nigerian, 17% England, Wales, NorthWestern Europe, 10% Portugal, 2% Spain, 1% Indigenous Puerto Rico, Indigenous Haiti, Dominican , French and so on. My family is from the island so reading history this does not surprise me that there are indeed a variation of Puerto Rican’s. Especially why some are lighter than others. Thank you for this article. It helps me to continue my research.


So Strange, everyone seems to know the truth about The colonization of the Caribbean islands/SA except some of the Hispanics that live there. The Spaniards ruthlessly went into the Caribbean/ SA and destroyed nearly half the population or more with diseases. They raped pillaged and enslaved all of the indigenous Indians. took away their language and culture and replaced it with Spanish and Christianity.
The Spaniards were devils to the original inhabitants of Puerto Rico and yet Many Puerto Ricans still want to be called Spanish. No one in Spain calls any one from the colonized islands Spaniards. I’ve always found this phenomenon odd want to be something you are not and also something you will never be accepted as, instead of finding your true history which is where your true strength will always lie. Read:


Yo llebo tantos año en los estados unidos que é perdido mucho de mi cultura pero la culpa de esto es solo mía. Yo amo mi isla cada vez que visito me quiero quedar mi corazón siempre será boricua Taina eso no me lo quita nadie. Hace como un año yo me hice la prueba del DNA y como dice el artículo yo soy native american (taíno) Spaniard,Portuguese,Afro, y Otis más que no me puedo accordar mis padres son noticias nacidos y criados. Yo tengo dos hijos mi hija se hizo la prueba y aún siéndolo cuarta generación su por ciento de Native American es bastante significante ella también es muy orgullosa de llamarse taíno. Perdonen mis errores dramáticos y gracias por permitirme hablar de mi herencia

Nawah Rawchaa
Nawah Rawchaa

You’re Israelites