The aims of the present research were to estimate the amount and distribution of genetic diversity within and among Fritillaria tubiformis subsp. moggridgei populations from north-western Italy using RAPDs, and to evaluate possible effects of habitat fragmentation on genetic variation. The genetic relationship between the subspecies and Fritillaria tubiformis var. burnatiihas also been investigated. Spatial structure and the expected association between genetic and geographical distances among populations were assessed, in order to provide recommendations for in situ preservation of the species.