Mexican villagers believe they represent their ancestors' souls
Dr Lincoln Brower, a specialist in the species, said "this was the worst episode of butterfly mortality" he has seen in 25 years of studying the insects.
The World Wildlife Fund said the Monarchs, which died last month, were killed by a combination of cold weather and rain.
Millions of butterflies make the annual flight of up to 3,000 miles from Canada or the United States to Mexico.
Incredible journey
They leave North America in the spring and arrive in the pine forest havens in Michoacan, west of Mexico City in October or November.
Their arrival coincides with Mexico's Day of the Dead celebrations. Many villagers believe the butterflies represent the spirits of their ancestors.
Scientists are worried that if this North-South migratory population is wiped out it will prevent them from solving the mystery of how the Monarchs know to follow the same route every year.
Logging threat
Dr Brower said deforestation may have exacerbated the cold snap's effect on the butterflies by reducing the forest canopy which helps to regulate temperature.
"The government should declare a moratorium of logging in the sanctuaries. They have to stop deforestation," said Mexican environmentalist and poet, Homero Aridjis.
But Dr Brower added that America, where some of the Monarchs begin their journey, and others pass through, is not blameless.
"I think the big lesson is that in the United States... the real threat are the herbicides killing the milkweeds and other plants the monarchs use for food."