We have analyzed three Creole goat populations from Peru, Mexico and Chile using microsatellite markers. We have also analyzed the genetic relationship between them and Murciano-Granadina and Malagueña Spanish goat breeds. The average number of alleles per locus was similar in all populations (7.3) except the Chilean Creole (5.1). This Creole goat population has presented the lowest value of observed (Ho) (0.53) and expected (He) heterozygosis (0.59). The Peruvian Creole has presented the highest values of Ho (0.70) and He (0.71). We have found a scarce level of genetic differentiation between goat populations (FST= 0.069) being more important the individual genetic differences due to crossbreed with several breeds. The Peruvian Creole was closed to analyzed Spanish breeds, followed by Mexican Creole. Finally the Chilean Creole was the most distant to the others populations.