A total of 111 individuals (79 females and 32 males) of the endangered Catalonian donkey breed were analysed by using a commercial equine paternity polymerase chain reaction typing kit. Eleven of the 12 horse microsatellites were amplified when using donkey's DNA. One locus, ASB2, did not amplify in any sample. The allele range for HTG4 overlapped with HMS7 and their results could not be interpreted. The mean number of alleles detected per locus was 7.7 (±1.0), being the average of genetic diversity detected in the population, and measured as the unbiased average expected heterozygosity (He), of 0.712 ± 0.038. All the analysed loci showed disagreement with Hardy-Weinberg proportions except HTG7 (from permutation tests). The within-population-inbreeding estimate was highly significant (p < 0.001) and equal to 15.4% (as measured by Fis-statistic). The cumulative exclusion probability was 0.999. The deficit of heterozygotes can be partly explained by a population subdivision effect (FST - 3.5%), although the main factor that has provoked this lack of heterozygotes can be attributed to consanguinity.