In this study, we examined the gut contents and morpho-histology of the digestive tract of Neostethus lankesteri Regan, 1916 to examine habitat utilization. Thirty individuals of N. lankesteri were collected monthly from two sites: Pranburi River estuary (PRE) and Sirinart Rajini Mangrove Ecosystem Learning Center (SRMELC), during the Northeast and Southwest monsoon season. Based on gut contents analysis of N. lankesteri, the primary food items were categorized as follows: diatoms, dinoflagellates, other microalgae, and zooplankton. The index of relative importance, IRI, showed that diatoms were a major component followed by zooplankton at the PRE site, whereas zooplankton was a major component followed by diatoms at SRMELC during the two seasons. Moreover, N. lankesteri had a superior mouth with canine teeth. The pharyngeal tooth plates were numerous and canine shaped. The intestine coefficient of N. lankerteri was 0.55, which is consistent with omnivory. Histology of the digestive tract in N. lankesteri showed that they were stomachless, while the intestine consisted of three regions: anterior, middle, and posterior. Collectively, gut content and morpho-histological analyses from our studies indicated that N. lankesteria is an omnivore, feeding on multiple trophic levels depending on their availability.