The diatom genus Microcostatus, initially distinguished from Navicula sensu lato based on Navicula krasskei Hustedt, currently comprises 27 established species worldwide. However, the phylogenetic position of this genus continues to be undetermined. Our study utilized light microscopy, scanning and transmission electron microscopy, along with SSU rDNA and rbcL gene sequencing, to describe two novel species. M. hainanensis L.Y. Tan, Y.H. Gao & C.P. Chen was collected from a Haina sand beach. M. witkowskii H.N. Lin, Y.H. Gao & C.P. Chen was obtained from a Fujian esturine mangrove. Both are small (valve length 2 - 13 μm) with rounded ends and a slightly curved filiform raphe. Additionally, both species possess two axial depressions on both sides of the raphe sternum. Striae that form macroareolae are externally occluded by perforated hymenes. Striae exhibit a distinct radial pattern but are absent at the center of the valve in M. hainanensis, whereas they are nearly parallel and continuous with microcostae in M. witkowskii. Furthermore, microcostae are scarcely discernible and a conopeum is absent in M. hainanensis, whereas microcostae and unperforated conopeum are obviously present in M. witkowskii. Molecular phylogenetic analyses have indicated that these two species are members of the Sellaphoraceae family, rather than the Naviculaceae family. On the other hand, the paired, lateral plastids in M. hainanensis and M. witkowskii differ from the single H-shaped plastid found in the Sellaphoraceae, suggesting a more extensive phylogenetic relationship.