Mission Animals and Livestock / Mission Brands

How many different kinds of animals were at Mission San Juan Capistrano?

All of the missions had extensive livestock herds. San Juan Capistrano had large numbers of cattle (ranging between 10,000 - 14,000 head during their peak years of 1806-1827) and an average of about 12,000 sheep during the same years. Their annual reports show some goats (203 in 1820), pigs (195 in the same year) and of courses horses (about 140 on average), which we used for transportation. While San Juan Capistrano didn't have the largest herds of livestock in the mission chain, it was in the upper half.

How many of which types of animals were present at the Carmel Mission San Carlos de Borromeo?

San Carlos Borromeo de Carmelo was an extremely important mission because of its proximity to the capital of Alta California, in Monterey, and because it was headquarters for the mission chain from 1770-1803. However it did not have the large herds of livestock found at many of the other missions. On December 31, 1832, two years before secularization of the missions, the padres reported the following animals present:
Cattle 2,100
Sheep 3,300

What types of animals came to California with the padres, soldiers and settlers?

I have checked with a couple mission scholars to see what they can tell us. The consensus seems to be the missions and settlers probably did introduce both animals. Cats were used on Spanish ships to control rats. For much of the Spanish era, ships from San Blas (on the Baja peninsula) brought supplies and missionaries to California and a few wily cats may have escaped or been taken as pets. There is a story about one of the missionaries (Fr. Uria) who had a collection of cats. Dogs were used to control sheep on the mission lands. All of the missions had large livestock herds.