The current study was designed to establish the specie identification of the predominant Siphonaria species (S. asghar, S. belcheri and S. kurracheensis) via PCR based amplification of the two mitochondrial housekeeping genes i.e. 16S rDNA, COI, and one nuclear H3 gene. The nutritional significance of the Siphonaria sp. is also highlighted via amino acid profiling. Sampling was conducted at Buleji, the major coastal site of Karachi which harbours a huge and varied number of gastropods. The body muscle was dissected out of the shell and used for molecular identification and biochemical analysis (Amino acid profiling). Macro/micro morphology of the shells was also studied by scanning electron microscopy and energy dispersive X-ray spectrometry. The analysis of nutritional status of the three Siphonaria sp. revealed quite similar profiles among the three Siphonaria sp with the presence of nine essential and nine non-essential amino acids. Our results successfully established the method of molecular identification of Siphonaria sp. The study also showed that Siphonaria sp. are nutritionally rich and thus can be consumed as food or feed as valuable marine resource to overcome the malnutrition problem in the developing countries.