Because of the great number of small, more or less isolated, indigenous populations, Bosnia-Herzegovina represents a very interesting area for population-genetic surveys of different levels and approaches. Fascinating diversity of local human populations, as well as various levels of reproductive isolation can be attributed to simultaneous and interactive effects of a vast number of factors (geographical, ethnical, religious etc.). The very first known bioanthropological analyses of Bosnia-Herzegovina population conducted by Austro-Hungarian army doctors can be considered an initial phase in determining the genetic structure of this population. It is important to stress out that all of the preliminary studies were based, primarily, on the observation of phenotypic traits, such as blood groups, color blindness, the shape of lobule, PTC sensibility, thumb flexibility, or analysis of the effect of some factors that misbalance genetic equilibrium. The following phase that was relatively short was dominated by analysis of different cytogenetic markers. The very first steps in investigating variety of the fundamental, molecular-nuclear and mitochondrial DNA markers for diversity analyses of isolated Bosnia-Herzegovina populations were taken at the beginning of this century. Following analysis of STR markers variation, autosomal, as well as Y-chromosome markers, were completed in order to establish the referent sample and to incorporate the data about its molecular biodiversity in regional database (REBID-a). Finally, the most interesting and controversial results were obtained trough the observation of 28 Y-chromosome biallelic markers within in 256 Bosnian males.