We investigated five population pairs of Dalbergia sissoo in Nepal for variation of cpDNA and at the isozyme gene locus Gdh-A . Each population pair consisted of one natural population and a neighboring plantation. Two or three different cpDNA-haplotypes were observed in each population with a total of eight different haplotypes. The differentiation of cpDNA haplotypes between the group of natural populations and the group of plantations was almost complete. Thus, the plantations did not originate from any of the investigated natural populations, but reproductive material was transported over long distances during plantation establishment. All plantations proved to be fixed at the Gdh-A gene locus, which showed considerable polymorphism in natural populations indicating different adaptive potentials of plantations and natural stands.