The Anatolian black pine [Pinus nigra Arnold subsp. pallasiana (Lamb.) Holmboe var. pallasiana] is one of the subspecies of European black pine, growing naturally as a widespread mid-elevation species in the southern, western, and northern Anatolian Mountains of Turkey. Three well-recognized varieties [var. pallasiana, var. fastigiata Businsky with pyramidal form, and var. seneriana (Saatcioglu) Yalt. with globular-shaped crown with multiple stems] occur naturally, but the studies on them are very limited. These 3 varieties of Anatolian black pine were sampled in natural stands where they coexist to determine evolutionary divergence in the species as well as its evolutionary relationships with other related pine species. A total of 71 trees were sampled to assess molecular divergence patterns in the species by using 3 noncoding trn regions (trnL, trnL-F, and trnV) of chloroplast DNA. The results indicated that trnL and trnV regions were conserved among Anatolian black pine taxa, but the trnL-F region revealed 3 parsimony-informative sites. The sequence diversity in the trnL-F region was useful to separate both var. seneriana and var. fastigiata from Anatolian black pine as well as this species from the other members of section Pinus L. The genetic divergence between 2 varieties (0.0018-0.0027) was greater than the divergence between varieties and Anatolian black pine (0.0009-0.0018). The nucleotide sequences of trn regions obtained from seed megagametophytes of both Anatolian black pine and var. seneriana stands from the same location did not show any divergence, while the trn sequences from needle tissues of var. seneriana diverged from the trn sequences of Anatolian black pine. This divergence suggests that var. seneriana may have evolved as a result of a point mutation in a gene with pleiotropic effects involved in apical dominancy of Anatolian black pine, but this has to be explored further with future studies.