We analyzed the genetic diversity of populations of two sympatric species of Lymania (Bromeliaceae), both endemic to the Atlantic rainforest of southern Bahia (Brazil). Lymania azurea has a restricted occurrence, while Lymania smithii has a wider distribution. Our aim was to provide genetic data to contribute to the design of more efficient conservation strategies for these bromeliads, possibly justifying inclusion in the official Brazilian list of Endangered Species. Up to now, L. azurea has been classified by the Brazilian Ministry of the Environment as "data deficient". We sampled four populations of L. azurea throughout its distribution area in southern Bahia and two populations of L. smithii in the same region. Genotyping was performed with 48 random amplified polymorphic DNA markers. Based on the Jaccard genetic similarity index, L. smithii has greater diversity than L. azurea. An analysis of molecular variation showed greater genetic variance within than between populations for both species. L. azurea was found to have 20% inbreeding, probably due to population fragmentation, with L. smithii showing only 10%. When we analyzed pairs of populations of L. azurea within a conservation unit, we found low population structure (ФST = 0.098), apparently due to a large degree of gene flow between them. In disturbed areas, we found a higher ФST (0.372). We found low genetic variability for L. azurea, probably as a consequence of habitat fragmentation, supporting the need for its inclusion in the Brazilian list of endangered flora.