SUMMARY: Okinawan coasts are a rich source of biodiversity, including of filamentous cyanobacteria, owing to their habitat diversity created by coral reefs. Along the coastlines of Okinawa, several undescribed species, including those from Neolyngbya, remain unexplored. In this study, two undescribed cyanobacterial species with morphological resemblance to Neolyngbya were identified using a polyphasic approach. Both taxa had morphological features similar to known species of Neolyngbya; however, the cell size and thallus shape were different. Phylogenetic analyses of the 16S rRNA gene and the 16S‐23S rRNA internal transcribed spacer (ITS) region showed that the two new species formed a highly supported independent subclade within Neolyngbya. Accordingly, three informative domains of the ITS region (D1‐D1′, Box B and V3) also presented distinct secondary structures compared to previously described species of Neolyngbya, both in structure form and configuration. Overall, analyses of morphology and phylogeny of the 16S rRNA gene and the 16S‐23S rRNA ITS region, as well as the secondary structures of ITS region, supported the proposal of two new species within Neolyngbya. Herein, we propose N. intertidalis sp. nov. and N. latusa sp. nov. as new members of Neolyngbya under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants (ICN). [ABSTRACT FROM AUTHOR]