To estimate the diversity, structure and genetic flow in three colombian southwest afrodescendent populations (Buenaventura, Mulalo y Tumaco), the alleles revealed by 8 autosomal STR’s were analyzed in 78 no-related individuals, by the use of PCR and comparison with specific allelic ladders for every system resolved by polyacrylamide gel (8%). The results were compared with 2 amerindian populations (Awa-Kuaikier and Coyaima) and 2 mixed colombian populations (Valle del Cauca and Cauca). For the afrodescendent and amerindian populations was found moderate diversity (h between 0.768±0.414 and 0.796±0.424), in contrast, the mixed population showed higher rates (>0.803), which is probably caused by mixing with amerindians, that also can explain the high endogamy seen in mixed populations. The AMOVA exhibited moderate genetic structure between the afrodescendent populations (FST= 0.098; p<0.05), but higher between the three ethnical groups compared (FST=0.26723; p<0.05). The closer genetics distances are in favor of Tumaco and Buenaventura, supported for the migration rate found (34.298), which was the same inside of amerindian and mixed populations. Maybe, because Mulalo is a closed isolated population, its differences in front others afrodescendent populations are explained. The neighbor-joining tree showed nearest relations among amerindian and mixed populations, furthermore, the ancestral character for the afrodescendents. That sustains the idea of genetic flow maintained between the 3 ethnical groups, principally between amerindian and mixed populations, supported because the genetic differences, migration rates and amerindian matrilineality reported in the literature.