Pairs (18) of microsatelite primers were used in this study to detect the genetic relationship within Black Slavonian Pig and between Turopolje Pig, Mangalitsa breed and Croatian Wild Pigs. The second goal of this study was to determine phylogenetic relationships among these breeds and some Asian and European pigs using the mtDNA D-loop sequence polymorphism. The third goal was to determine the MC1R genotype of Black Slavonian pigs and to find an efficient and simple PCR-RFLP method, based on differences in MC1R genotype, to distinguish between purebred Black Slavonian pigs and their crossings with commercial pig breeds and Wild Boars. Aiming to conduct microsatellite analysis each animal was genotyped for 18 microsatelite markers, chosen based on their quality, size, polymorphism and location on the porcine genome as proposed by the FAO. Two pairs of primers amplified a 511-bp fragment of control region between sites 15 390 and 15 900 (Mit1.F and Mit1.R) and a 810-bp fragment between sites 15 825 and 16 634 (Mit2.F and Mi2.R) were genotyped for mtDNA. Two primer pairs were used to amplify the majority of the single exon of MC1R gene aiming to determinate MC1R genotype of Black Slavonian pig. The first pair of primers, MERL1 and EPIG2, was used to amplify a 428-bp product from the 5’ half of the exon, whereas EPIG1 and EPIG3 amplified a 405-bp product from the 3’ half. Our results showed that the 18 microsatellites used in this study were useful markers to study genetic diversity among Croatian autochthonous pig breeds. This set of microsatellites may be used for identifying individuals and for genetic diversity studies for selection and conservation of the Black Slavonian pig, Turopolje pig and Mangalitsa breed. Genetic distances between populations made with Principal Component Analysis (PCA) method noticed that studied populations are mostly clearly geneticaly defined. mtDNA analysis suggested that Black Slavonian and Turopolje pig showed genetic distances from the other European and Chinese pig breeds. Black Slavonian and Turopolje pig clustered together. Mangalitza was used in the development of Black Slavonian pig and this can explain their presence in clustering. Also, with this work, we were able to identify a simple PCR-RFLP method, based on different coat color MC1R gene genotypes, by which it is possible to detect potential crossings of autochthonous Black Slavonian pig with commercial pig breeds and including wild boars.