The genetic relationships and species boundaries of three species of Aerobryopsis, including a new one and a closely related taxon, Aerobrydium filamentosum within the Meteoriaceae of the Western Ghats of India were estimated based random amplified polymorphic DNA (RAPD) markers and morphological characters. Using 12 decamer primers 72 RAPD markers were identified, of which 69 (96%) were polymorphic. Amplicons of the primers OPF-01 and OPD-08 served as distinct markers to discriminate the species of Aerobryopsis and Aerobryidium filamentosum. The multivariate analyses of morphological and molecular data indicate that all the samples belong to four distinct species. RAPD proved to be a useful tool to detect genetic relationships of these closely related taxa and Aerobryopsis eravikulamensis Manju & Rajesh, a new taxon, is illustrated and described.