The family Mastacembelidae (Teleostei: Synbranchiformes) is a group of eel-like freshwater fish, having a snout which is extended into a proboscis, a series of well-separated spines and lack of pelvic fin. This family represents a diverse species composition separated by three genera which is distributed throughout tropical and subtropical regions of Africa and Asia. Variation and overlapping in morphological and anatomical characters as well as diverse habitat have resulted in formation of several species complexes, cryptic species and misidentification in Mastacembelids. Hence, this project attempts to construct phylogenetic relationships among 16 species (Mastacembelus and Macrognathus) of Asian Mastacembelids collected across South and Southeast Asia by using S7 ribosomal protein intron (RP1) and cytochrome b sequences. Our data recovered three major lineages within Macrognathus and a lineage within Mastacembelus with some internal nodes remaining poorly resolved. High intraspecies genetic variation was found in several species. Thus, the resolution of species boundaries is far from resolved and requires further study i.e morphological characters and additional molecular markers. The phylogenetic relationships within the family and existing taxonomic problem are discussed. This ongoing study will provide critical information in resolving mastacembelidae taxonomic uncertainties, understanding the geomorphological history of Southeast Asia and formulating conservation priorities in the face of ongoing and escalating environmental deterioration across this bio-cultural hotspot.