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Understanding microhabitat use of an organism is an important first step to understanding its ecology and also provides critical information for guiding management and conservation efforts. Most microhabitat studies of freshwater fishes have focused on temperate systems, with far less research on fish microhabitat use in tropical streams. Here, we studied microhabitat use and selectivity patterns of juvenile Mugil cephalus within a Hawaiian stream, USA (Waiähole Stream, latitude: 21.48°, longitude: −157.85°). We measured depth, velocity, substrate composition, and canopy cover at locations where M. cephalus was observed feeding and compared attributes of these locations to microhabitat available to the fish. We found significant differences in microhabitats where mullet fed compared to microhabitats available, with feeding occurring in microhabitats with moderate velocities (0.21–0.60 m /sec), shallow to moderate depths (0.31–0.80 m), gravel and pebble as dominant substrates, and low canopy cover. Results of our study suggest that juvenile M. cephalus are selecting erosional habitats and avoiding depositional habitats, a result that was also supported by a multivariate analysis of habitat selectivity. Our data corroborate results of other studies reporting that fish grazers select habitats that are clean (erosional) rather than silted (depositional). Knowing how M. cephalus in streams use the available habitats is important for understanding how to manage freshwater habitat to support juvenile M. cephalus in the face of increasing anthropogenic impacts and a changing climate.