Western Visayas has largest population of native chickens in the Philippines; however, data on the phenotypic and genetic diversity is limited. Eight hundred and ten chickens from 270 different flocks, from six provinces within the region were chosen for characterization. Data collected includes farmer selection practices, means of identifying genetic groups and information on phenotypic traits of native chickens. This information was analysed using statistical tools suggested by FAO. Phenotypic diversity and equitability of distribution were analysed using Simpson's diversity index and equality of distribution. Results showed that native chicken genetic resources are comprised of two types, the Jolo and Bisaya; the latter was further divided into Bisaya–Cluster I and Bisaya–Cluster II. Jolo chickens were the heaviest (P < 0.01) but comparable with Bisaya–Cluster II in terms of egg weight, head shape and phenotypic distance. They all had higher diversity and equitability of distribution in their plumage colour and pattern, though the iris and shank colour had higher diversity but had limited distributions. Bisaya–Cluster II and Jolo chickens had higher diversity and above average distribution in liveweight. They were also homogenous in feather morphology and distribution; head and breast shape, and skeletal variants. Thus, the observed diversities and distributions can be used in identifying genetic materials for any breeding undertakings.