What effect did the small pox have on the indians of the mission if any?

Periodic smallpox outbreaks and other European diseases affected the Indians particularly hard as they had no immunity. Experts estimate that European diseases accounted for about one third of the deaths of Native Americans in California after the Europeans arrived.

Sadly, this phenomenon was not unique to California and even more severe among other Native American populations.

In 1617–1619, for example, smallpox wiped out 90% of the Massachusetts Bay Native Americans.It reached Mohawks in 1634, Lake Ontario in 1636, and the lands of the Iroquois by 1679.

Smallpox epidemics in 1780–1782 and 1837–1838 brought devastation and drastic depopulation among the Plains Indians.

By 1832, the federal government established a smallpox vaccination program for Native Americans (The Indian Vaccination Act of 1832). At this time, of course, California wsas still part of Mexico.