A total of 130 heads of native chicken from the entire province of Bohol were randomly sampled to determine the phenotypic characteristics, including qualitative and quantitative traits, of the Boholano genetic group of the Philippine native chicken. Results showed variations in the qualitative traits of the Boholano genetic group. However, it is noted that Boholano genetic group was predominantly of single comb, orange-colored iris, white skin, yellow shank and red-plain plumage. Although the quantitative traits of Boholano genetic group were not significantly different across the province of Bohol, the roosters were significantly heavier and had higher body measurements than the hens (P<0.01). Twenty four native chickens and a commercial layer strain were used to evaluate the genetic characteristics of the Boholano genetic group. Sixteen microsatellites were used but only 13 microsatellite markers were found to be polymorphic. The 13 microsatellites, distributed to eight linkage groups, had 4-8 alleles detected per locus. The high mean number of alleles per locus, observed heterozygosity and expected heterozygosity, negative inbreeding coefficient and high fixation coefficient of a subpopulation within the total population values show the high diversity of Boholano genetic group of Philippine native chicken.