The spatial genetic structure in three subpopulations of the endangered clonal plant Iris sibirica from southern Poland was investigated. The subpopulations occurred in different habitats, i.e. in a Molinietum caeruleae community, a Phragmites australis patch and in a willow brushwood. Using 13 enzymatic systems, sixteen loci were evaluated. The very low genetic diversity (P = 0%–18.7%, A = 1.0%–1.19%, H_o= 0.000–0.009) observed within the subpopulations is probably due to lack of recruitment, habitat fragmentation and/or historical causes. Five distinct multilocus genotypes, detected from 148 collected samples in the subpopulations, supported this observation. This fact illustrated that only clonal growth could maintain the present low genetic variation through the domination of a single or a few clones within these sites. Moderate genetic differentiation (F_ST = 0.077, P < 0.001) that varies strongly between pairs of subpopulations, was observed, thereby suggesting substantial gene flow between populations.