Halamphora siqueirosii sp. nov. is a marine benthic diatom isolated as a monoclonal culture from a hypersaline evaporation pond at the Guerrero Negro Saltworks, Baja California Sur, Mexico. Analysis of the valve ultrastructure of this taxon using light and electron microscopy indicated that its uniseriate striae and the density of its dorsal striae are useful characteristics for discriminating H. siqueirosii from other species with similar morphological patterns. The phylogenetic analyses performed with nuclear ribosomal genes, the small (18S) and large subunits (28S), and chloroplast gene ribulose-bisphosphate carboxylase (rbcL) fragments showed that H. siqueirosii is closely related to H. americana, H. calidilacuna and H. incelebrata. Morphological differences between this new species and similar ones are discussed.