The study of food composition and feeding ecology of fishes living in the intertidal zone are essential in understanding the energetic connectivity between terrestrial and aquatic ecosystems. The mudskipper Periophthalmus waltoni is an amphibious fish in the intertidal zone. The aim of this research was to discern how spatial and temporal factors influence the species' diet. A total of 319 individuals were collected across two estuaries in Hormozgan province (184 in Bandar Abbas and 135 in Bandar Khamir) during November 2018 to April 2018. The results revealed that P. waltoni primarily follows a carnivorous diet, as indicated by their relative gut length (RLG) and diet composition. The individuals measured 9.2–11.8 cm in total length and 8.1–15.8 g in weight. Analysis of stomach contents identified three main preys: Uca, Gastropoda, and Coleoptera, with Bandar Abbas and Bandar Khamir showing a prevalence of crab (79.31%) and Gastropod (54.16%), respectively. The mudskipper's feeding strategy, as per Castello, appeared general in Bandar Abbas and specific in Bandar Khamir. The highest frequency index of prey occurrence for specimens in Bandar Abbas for crab prey was calculated at 68.31%, while in Bandar Khamir, it was determined as 42.52% for gastropods. Stomach emptiness index values of 21.49% and 13.86% suggest P. waltoni is a voracious feeder.