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The present study provides the first comprehensive embryonic development of the freshwater Syngnathid fish species, Microphis deocata (Hamilton), a Near Threatened pipefish endemic to the Brahmaputra River drainage in Northeast India and Bangladesh. Microphis deocata is a Gastrophori species as the males develop an abdominal brood pouch. Mature individuals were collected and maintained in well‐aerated aquaria under controlled conditions to induce natural spawning. The number of eggs within the males' brood pouch ranged from 17 to 22 (for n = 10), measuring 0.7–1.0 mm in diameter. A total of 10 developmental stages could be recognized under four developmental periods namely, early embryogenesis, eye development, snout formation and juvenile. However, sensitivity, and therefore mortality, while handling of this species restricted the study from reporting the exact time intervals for stages following the blastodisc formation ~48 hr post fertilization. A newborn larvae measures ~14 mm and is free‐swimming with distinct dorsal fin (with 31–32 rays) and a sector‐shaped caudal fin (with 8–9 rays). The study aims to provide baseline information on the embryology of M. deocata in culture condition which will be helpful for future studies on conservation biology, population status and management of this species. [ABSTRACT FROM AUTHOR]