a b s t r a c t The aim of the present study was to estimate the genetic intra-breed variability of Churra tensina and Churra lebrijana endangered breeds and to establish genetic relationships with Churra, Latxa and Merino breeds, as well as Spanish mouflon, by using 28 microsatellite markers, to provide useful information for their conservation. Allele frequencies and het-erozygosity revealed high genetic variation in the two endangered breeds despite their small population size. Estimates of inbreeding coefficient (F IS) were significant for all breeds studied, except for Churra lebrijana breed. The highest inbreeding coefficient (F IS = 0.143) was found in the Spanish mouflon. Genetic differentiation tests (F ST = 0.121) and assignment of individuals to populations indicated the existence of defined breed populations, and low genetic flow between these breeds. The highest pairwise Reynolds distance (D R) values were observed between Mouflon and the domestic sheep breeds. Considering only domes-tic sheep breeds, the Churra lebrijana breed showed the highest pairwise D R values . The lowest values were found between Latxa and the other domestic sheep, except for Churra lebrijana. Results of pairwise D R values, as well as phylogenetic tree and bottleneck analysis showed an important genetic isolation of the Churra lebrijana breed from the other Churra types, and genetic signatures of a demographic bottleneck. Finally, structure analysis of populations detected a population subdivision in the Latxa sheep breed. In conclusion, this study presents valuable insight into the existing genetic variability of two Spanish endan-gered breeds, as well as the first study in Spanish mouflon based on microsatellite analysis. The high degree of variability demonstrated in Churra tensina and Churra lebrijana implies that these populations are rich reservoirs of genetic diversity.