The Nemipteridae fish family is a colored marine fish species having elongated bodies and filamentous dorsal fin extensions. They are widely distributed in the Indo-Pacific Oceans and prefer to live in shallow coastal waters, often over muddy and sandy bottoms. This fish family has economic value in Southeast Asia and is widely consumed as food. In this study, we conducted the DNA barcoding of the Nemipteridae fish family. Five different species of Nemipteridae were taken from the marine waters of Pakistan. A total of 33 specimens belonging to five species and three genera were collected from 2019 to 2023. This study delineated two cryptic species (Nemipterus japonicus and Nemipterus randallii) on the molecular basis. The phylogenetic tree was made and showed genus-wise clustering of the species. A clear sister clade was able to be seen within the N. japonicus and N. randalli, Moreover, the barcode gap showed a significant genetic gap between these species, validating them as separate species. The present study of DNA barcodes has demonstrated high efficiency in the identification of species. This is the first study that explores the genetic basis of the family Nemipteridae from the coastal area of Pakistan.