Nummulitidae are the largest extant calcareous Foraminifera, and are widely distributed in tropical and subtropical shallow-water seas. Classical morphology-based taxonomy divides the Nummulitidae in two subfamilies, the Nummulitinae and Heterostegininae, according to the presence or absence of secondary septa. To test the evolutionary importance of this morphological feature, phylogenetic relationships of five Recent nummulitid genera were investigated by sequencing fragments of the SSU and LSU rRNA gene. According to our results, species characterized by septate chambers (Heterostegina depressa, Planostegina operculinoides, and Cycloclypeus carpenteri) either group with species lacking septate chambers (Operculina ammonoides, Nummulites venosus) or branch separately. This suggests that chamber subdivisions developed several times independently in the evolutionary history of the Nummulitidae, providing an example of parallel evolution in Foraminifera.