||Genetic diversity was assessed in the Portuguese native breeds of goats Algarvia (AL), Bravia (BR), Charnequeira (CH), Preta de Montesinho (PM), Serpentina (SP) and Serrana (SR), by analyzing 25 microsatellite markers in 193 animals. Genetic variability was high, with means for expected heterozygosity of 0.70 across loci, and nearly 7.0 and 4.4 for total and effective number of alleles per locus, respectively. The six breeds analyzed had similar levels of genetic variability, and the estimated FST was 0.031, indicating that, with the neutral genetic markers used, the proportion of genetic variability accounted for by differences among breeds is small. Depending on the breed considered, between 0.16 and 0.28 of the loci presented significant departures from Hardy–Weinberg proportions, mostly because of a deficit in heterozygosity, with a significant positive FIS in most breeds, particularly in PM. The dendrogram based on Nei's standard genetic distance and the analysis by principal components indicate a separation of AL and BR from the remaining breeds, with some clustering of PM with SR, and of SP with CH, in agreement with their geographical distribution. Individual distances based on allele sharing indicate that only AL and BR animals tended to cluster together, while overlapping was common for the other breeds. The analysis with STRUCTURE confirmed the separation of AL and BR, which were more closely identified with independent clusters of potential ancestral populations. For the other breeds, there was clear evidence of admixture, with various ancestral populations contributing differently to the current breeds. Evidence was found of a geographical cline, with a given ancestral population contributing more to breeds located nearby, and with a declining contribution as the geographical distribution of breeds became more distant. Our results indicate that native breeds of goats in Portugal present high levels of genetic diversity, but the differentiation among closely located breeds is weak. Some of the breeds show signs of genetic erosion, which imply the need for urgent measures of conservation and sustainable management of their gene pool.