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According to recent taxonomic treatments, Bromeliaceae subfamily Pitcairnioideae comprise the genera Deuterocohnia, Dyckia, Encholirium, Fosterella and Pitcairnia. We present a dated molecular phylogenetic analysis of a comprehensive taxon set to enable inferences of evolution in the subfamily. Phylogenetic relationships in Pitcairnioideae were reconstructed based on three plastid loci (rpl32‐trnL, rps16‐trnK, 5′ end of matK) and the nuclear single‐copy gene PHYC exon 1, using maximum parsimony, maximum likelihood and Bayesian inference. The plastid phylogenetic analysis supports the monophyly of the subfamily, whereas the nuclear DNA data suggest a nested position of Puyoideae in Pitcairnioideae. Fosterella and Dyckia (including Encholirium) are monophyletic in both analyses, whereas Deuterocohnia is paraphyletic and Pitcairnia remains unresolved in the plastid tree. A Bayesian relaxed clock model applied to the plastid data indicates a diversification of Fosterella and Pitcairnia at c. 6–8 Mya, whereas Deuterocohnia and Dyckia might have diversified at about 2–4 Mya. Our data support the concept that Pitcairnioideae originated in the Andes, followed by numerous dispersal events to South and Central America. Plastid capture events might explain the contrasting topologies of plastid and nuclear trees in Deuterocohnia, whereas the position of Puya needs to be re‐evaluated with additional nuclear markers.

The 15 SSR markers developed for F. rusbyi are promising candidates for population genetic analyses within F. rusbyi and other species of Fosterella.

The strong genetic differentiation between southeastern Caatinga and the remaining regions may indicate the occurrence of a cryptic species in . The unique genetic composition of each inselberg population suggests in situ conservation as the most appropriate protection measure for this plant lineage.

The set of 12 cpSSR markers provides a toolbox to analyze phylogeographical patterns of Dyckia species.

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In the Atlantic Rainforest located north of the São Francisco River (northeast Brazil), the humid enclaves called brejos de altitude play a significant role in the diversity dynamics of local flora and fauna. The related species Dyckia pernambucana and D. limae (Bromeliaceae) are characterized by their narrow endemic occurrence in such brejos, and their species status remains unclear. In order to understand the species delimitation in those assigned taxonomic entities, patterns of gene flow and genetic variability were calculated using nuclear and plastid microsatellites and AFLP markers. In this regard, we collected populations of the Pernambuco complex (D. limae and D. pernambucana, from the Borborema Plateau) and the closest relative D. dissitiflora (from the northern Espinhaço Range). Genetic diversity was moderate, despite the possible influence of genetic drift and selfing rates. Dyckia limae could not be undoubtedly discriminated from the remaining populations of Pernambuco, and we propose the synonymization of these species. Thus, the conservation of D. limae as a formerly single species would not reflect the conservation of the minimal gene pool of the studied lineage (D. pernambucana). We also propose the revalidation of the conservation status of this species, endemic to anthropomorphic island-like mountains environments. Finally, the associations found here were consistent with the historical patterns of colonization and fragmentation of the Atlantic Rainforest.