Brazilian naturalized goat breeds are adapted to the semiarid conditions prevalent in the Northeast region of the country (which has the largest Brazilian goat heard) and represent an as yet uninvestigated source of genetic diver-sity. Currently, imported goat breeds are crossed with Brazilian naturalized goat breeds, endangering the genetic po-tential of the naturalized breeds. We used 11 microsatellite markers to determine the genetic diversity among imported (non-naturalized) dairy Alpine and Saanen goats and naturalized Brazilian Moxotó goats. We genotyped 292 goats from three herds (one private, one from the University of Minas Gerais and the Moxotó conservation herd from Embrapa Caprinos) and found that the general heterozygosity was 0.6952 for Alpine, 0.7043 for Saanen and 0.4984 for Moxotó goats. The number of alleles ranged from 5 (INRA005) to 11 (BM3205), with an average of 7 al-leles per locus in the imported breeds and 3.5 alleles per locus in the Moxotó breed. Mean differentiation between populations was higher for herds (F ST S = 0.0768) than for breeds (F ST P = 0.0263), indicating similarity between the imported breeds and the existence of crosses between them. Nei's genetic distance was highest between the Moxotó breed and the imported breeds. These indicate that further studies using these molecular markers would be fruitful.