The genetic structure of Cereus peruvianus populations descended from cultivated plants (F(1) populations) and from plants regenerated in vitro (R(1) populations) was analyzed using α- and β-esterase isozymes in native PAGE. The estimated proportion of polymorphic loci was higher (50%) in the R(1) populations than the F(1) populations (42.85%). The mean observed (0.5599) and expected (0.5620) heterozygosity in R(1) descendents was also higher than the rates in F(1) descendents (H (o) = 0.4142; H (e) = 0.4977). A low level of population differentiation was detected in R(1) descendents (F (st) = 0.05). In contrast, population differentiation was high in F(1) descendents (0.2583). Esterase analysis using PAGE showed that artificial selection by silvicultural management provides high genetic diversity and a large genetic basis for C. peruvianus, whereas in vitro selection from callus tissue culture involves an increase of heterozygosity levels in descendents from somaclones and a low level of interpopulational divergence.