Eleven populations of black pine (Pinus nigra Arnold subspecies pallasiana) were studied at 17 polymorphic isoenzyme gene loci. The mean number of alleles per locus (A) was 1.6. Observed heterozygosity (H-obs) was the lowest in the Gurgendag population from Kazdagi (0.119) and the highest in the Qamhyayla population from Bolkar Mountains (0.287). The expected heterozygosities (H-exp) ranged from 0.296 (Asar, from Kazdagi) to 0.181 (Cehennemdere, from Bolkar Mountains). F-ST was 0.0592 for Kazdagi and 0.0358 for Bolkar Mountains. F-IS value was -0.25 in Bolkar Mountains and 0.42 in Kazdagi, indicating considerably less heterozygosity in Kazdagi populations than expected. There were significant deviations from Hardy-Weinberg expected frequencies in some of loci in both Kazdagi and Bolkar Mountain populations. The deviations in Kazdagi populations were due to excess of homozygotes while they were due to excess of heterozygous genotypes in Bolkar Mountains. The estimated genetic distances between populations ranged from 0.003 to 0.666. According to the genetic distance results, populations of Kazdagi form a genetically distinct group compare to the populations of Bolkar Mountains. Based on genetic diversity and distance statistics, three populations from Kazdagi (Asar, Mihlidere and Gurgendag) and two populations from Bolkar Mountains (Ulukisla and Gulekdere) are suggested as potential in situ conservation sites.