In the present study, we estimated the genetic diversity and relationships, as well as the propagation routes, of Madagascan goats using mtDNA control region and SRY gene sequences. The mtDNA sequences of 40 Madagascan goats revealed 10 haplotypes and a quite low nucleotide diversity (0.0014), suggesting a founder and/or bottleneck effect resulting from goat migration to Madagascar island. The analysis of sequences identical to Madagascan haplotypes indicated close genetic relationships between goats from Madagascar and Africa. Sequence analysis of the SRY gene in 40 male Madagascan goats revealed two haplotypes: Y1A (45%) and Y2A (55%). The paternal result indicated genetic influences from Africa, South Asia, and the Near East proximal to Madagascar. The analyses of the mtDNA control region and SRY gene sequences suggested a genetic relationship between Africa and Madagascar. Moreover, SRY sequences indicated influences from South Asia and the Near East. These phylogenetic results provide important genetic information for elucidating the propagation routes of Madagascan goats.