The present study aimed at the genetic characterization of five major goat populations of Sri Lankaincluding four indigenous populations (Jaffna Local – JFL, Kottukachchiya – KOT, Southern – SLS andNorth Central – SNC) and one stabilized crossbred (German Boer x indigenous goats, also known as “SriLankan Boer” – SLB). Genetic diversity was evaluated using 15 microsatellite markers and the mitochon-drial DNA D-loop variation. Allelic diversity and observed and expected heterozygosities were moderate,but less than Eurasian and Indian goat breeds. The overall mean estimated inbreeding coefficient (FIS)was 0.069 and significant heterozygote deficiency was detected in JFL (P < 0.001), KOT (P < 0.01) and SLS(P < 0.05), indicating population-specific drift or selection of the loci assessed. Genetic differentiationamong populations was low and the phylogenetic clustering pattern was in line with the geographicallocation of goat populations. Although pair-wise Cavalli-Sforza and Edwards chord distance clustered SLSand SLB separately from the rest of the populations, Bayesian clustering clearly showed lack of discretegenetic structure in Sri Lankan goat populations despite significant morphological and phenotypic differ-ences among them. Mitochondrial DNA D-loop sequences revealed significantly high haplotype diversitywith the existence of maternal haplogroups ‘A’ and ‘B’. Analysis of mtDNA sequences indicated maternalorigins of Jaffna Local, Kotukachchiya and Sri Lankan South distinct from the other goat populations.