Providing nursery habitats to a number of marine fish larvae that recruit after prolonged pelagic larval duration, has been identified as one of ecosystem services rendered by estuaries and protected inshore water bodies like mangroves, mudflats, swamps, and marshes. Larval fish congregation and survival are largely dependent on abiotic and biotic potential of such systems and many migrant marine fishes are adapted to them. However, occurrences of larval forms of tropical reef-associated vagrant species which are known for extensive range adaptations generate considerable academic interest. The present study provides the first report of ontogenic habitat utilization of yellow fin surgeon fish, Acanthurus xanthopterus Valenciennes 1835 in a tropical microtidal positive estuary, the Vembanad lake, South India. Surface plankton collections from the downstream part of the estuary revealed considerable proportions of acanthurid larvae in post monsoon (mean 354 ± 180 numbers/100 m3) and pre monsoon (mean 217 ± 120 numbers/100 m3) while they were absent in monsoon season. These acronurus larval forms were morphologically identified and sorted before being subjected for DNA barcoding. Mitochondrial DNA COI sequences developed from morphologically characterized acronurus larvae exhibited genetic congruency to sequence of A. xanthopterus which was evident from phylogram (bootstrap support of 100) and genetic distance data (intraspecific distance of 0%). The study indicates that Acronurus larvae of A. xanthopterus, after extensive cross-habitat dispersal, utilize the estuarine habitat to promote potential growth.