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The Iberian Peninsula is home to a large number of endemic species that often show strong genetic subdivisions which indicate possible isolation of populations in the past. Numerous phylogeographic and phylogenetic studies on Iberian flora and fauna have revealed this territory to be the origin of genetic differentiation during the Pleistocene Ice Age. To better understand the influence of Plio-Pleistocene climatic oscillations on the cladogenesis and population structuring of refugial taxa restricted to freshwaters of the Iberian Peninsula, we studied the evolutionary history of the small European genus Baldellia, both from a phylogenetic/phylogeographic perspective and regarding its ecological characteristics. Molecular analyses were based on four plastid regions and nuclear ITS2 ribosomal spacer from individuals belonging to geographically isolated Baldellia populations, while the relationships between climate and Baldellia species distribution was investigated by redundancy analysis applied to the climatic data with the occurrence of Baldellia species as external variables. The absence of a clear phylogenetic signal most likely reflects a common and recent cladogenesis for Baldellia. In contrast, the more rapidly evolving plastid sequences indicate a recent phylogeographic history of refugial repartition and ecological segregation probably occurring during the last glaciation, a scenario well supported by marked differences in species' ecological preferences and climate analysis. [ABSTRACT FROM AUTHOR]