Cocoliztli Epidemic (1545–1548): Catastrophe in New Spain

The cocoliztli epidemic of 1545–1548 was one of the deadliest disease outbreaks in the history of the Americas. Sweeping through central and southern Mexico, then the Spanish colony of New Spain, it killed a large share of the Indigenous population within a few years, with estimates commonly ranging from 5 to 15 million deaths. Its cause remains a subject of scientific debate.

Background

The Spanish conquest of the Aztec Empire in 1519–1521 was followed by repeated waves of disease. The smallpox epidemic of 1520 had already killed many people in Tenochtitlan and beyond, and measles followed around 1531.

By the 1540s the region was governed as the Viceroyalty of New Spain. Indigenous communities paid tribute and supplied labour to Spanish settlers through the encomienda system, and many were moved into new towns or set to work in mines and on building projects. Hunger, overwork and social disruption weakened people already living with high death rates.

Cocoliztli is a Nahuatl word meaning “pestilence” or “sickness”. Spanish writers adopted it as the name for this new and terrifying illness, which they did not recognise from Europe.

What happened

The epidemic began in 1545 and spread across the highlands of central Mexico and into Oaxaca and other regions over the next three years. Witnesses described a sickness that spread rapidly, killed within days and struck whole households at once.

The commonly reported symptoms included high fever, severe headache, bleeding from the nose, and, in some accounts, jaundice, dark urine and delirium. Many victims died within three or four days. The best clinical descriptions come from the physician Francisco Hernández, who observed and performed autopsies during the second great cocoliztli epidemic of 1576 in Mexico City, but chroniclers described the earlier outbreak in similar terms.

The Franciscan friar Bernardino de Sahagún, then at Tlatelolco, later wrote that he helped bury vast numbers of the dead there and that he fell gravely ill himself. Franciscan chronicler Gerónimo de Mendieta and others also recorded its severity. Accounts agree that Spaniards were seldom affected, while Indigenous towns were devastated.

The death toll

Exact figures are impossible because there were no reliable censuses. Most modern estimates place deaths between about 5 and 15 million, which would mean that perhaps half or more of the surviving Indigenous population of central Mexico died in some areas.

These figures rest on reconstructions of Mexico’s population that are themselves disputed. The historians Sherburne Cook and Woodrow Borah estimated that central Mexico had around 25 million people before the conquest and roughly one million by 1605; other scholars propose much lower starting figures. Whatever the exact numbers, contemporaries saw the 1545 epidemic as a catastrophe on a scale beyond anything before it.

The search for a cause

For centuries the disease was unidentified. In 2002 a team led by the Mexican epidemiologist Rodolfo Acuña-Soto, with the tree-ring scientist David Stahle, argued that cocoliztli was a native viral haemorrhagic fever, possibly carried by rodents. Tree-ring records showed severe drought in the 1540s and 1570s, which they suggested could have caused rodent populations to boom and spread infection after rains returned.

In 2018 a team led by Åshild Vågene and Johannes Krause analysed DNA from the teeth of people buried in an epidemic cemetery at Teposcolula-Yucundaa, a Mixtec town in Oaxaca linked to the 1545–1550 outbreak. They identified Salmonella enterica serovar Paratyphi C, a bacterium that causes enteric (paratyphoid) fever, spread through contaminated food and water.

The finding was the first genetic evidence for a pathogen in a colonial epidemic in the Americas, but it did not end the debate. Paratyphoid fever does not easily explain all the haemorrhagic symptoms reported, and the method could only detect certain pathogens. Some researchers think more than one disease may have been involved.

How contemporaries understood it

People in the 16th century had no concept of bacteria or viruses. Spanish physicians generally explained epidemics through the theory of the four humours, corrupted air (miasma) or the influence of the stars, and treated patients with bleeding and purges that could do more harm than good.

Many friars interpreted the deaths in religious terms, as a divine punishment or a trial, while also organising care and burials. Hospitals for Indigenous patients were few, and the main one in Mexico City, the Hospital Real de Naturales, was founded only in 1553; no institution could have coped with numbers on this scale. In many villages there was no one left healthy enough to nurse the sick or bring in food and water, which probably raised the death rate further.

Nahua communities also recorded the epidemic in their own annals and pictorial histories, which mark the years of great dying alongside other events such as famines and the installation of new rulers.

Myths and facts

A common assumption is that all the post-conquest epidemics in Mexico were smallpox. In fact, contemporaries clearly distinguished smallpox (in Nahuatl, huey zahuatl, “great rash”) from cocoliztli, and the symptoms reported for cocoliztli were different.

Another simplification is that the Salmonella study “solved” the mystery. The study identified one pathogen in one community, and its authors themselves noted that other diseases could have been present but undetectable with their methods. The cause of the epidemic across all of New Spain therefore remains uncertain.

It is also sometimes said that the Spanish deliberately spread the disease. There is no evidence of this for cocoliztli; the high mortality is better explained by disease combined with the harsh conditions of colonial rule.

Consequences

The epidemic deepened the demographic collapse of Indigenous Mexico. Fields went unharvested, tribute and labour obligations became impossible to meet, and many towns were left with only a fraction of their former inhabitants.

Labour shortages pushed colonial authorities to reorganise the economy. Over the following decades the encomienda lost importance and officials expanded the repartimiento, a system of rotating, state-allocated labour. Survivors from scattered settlements were later gathered into new, concentrated towns known as congregaciones, partly to make them easier to govern and evangelise.

The disaster also fed the growing demand for enslaved African labour in New Spain and changed the balance between Spanish, Indigenous and mixed populations. A second great cocoliztli epidemic in 1576–1580 struck the weakened population again.

Legacy

Cocoliztli is now a classic case in the history of epidemics and of the wider Columbian Exchange, the transfer of plants, animals and diseases between the hemispheres after 1492. It shows how disease, drought, violence and colonial exploitation could combine to produce mortality on an enormous scale.

The research at Teposcolula-Yucundaa also demonstrated how ancient DNA can help identify historical diseases, prompting similar studies of other colonial-era burials.

Timeline

• 1520: Smallpox epidemic devastates Tenochtitlan and central Mexico.
• c. 1531: Measles epidemic in New Spain.
• 1545: Cocoliztli epidemic breaks out in central Mexico.
• 1545–1548: The disease spreads across the highlands and into Oaxaca.
• c. 1550s: Teposcolula-Yucundaa is abandoned and its people move to a new town in the valley below.
• 1576–1580: A second great cocoliztli epidemic strikes New Spain; Francisco Hernández records clinical observations.
• 2002: Acuña-Soto and colleagues link the epidemics to drought and propose a haemorrhagic fever.
• 2018: DNA of Salmonella enterica Paratyphi C is identified in victims at Teposcolula-Yucundaa.

Why it matters

The cocoliztli epidemic of 1545–1548 was among the worst mortality events in recorded history and a turning point in the population collapse of Indigenous Mexico. Its mystery also makes it a landmark case for modern science, showing both the promise and the limits of genetic methods in explaining the past.