Pholis gunnellus (Rock Gunnel) is an amphibious fish found along North Atlantic coastlines. Remaining above the waterline at low tide and breathing air, it is ecologically unusual and is a food source for a variety of seabirds, mammals, and fish. We investigated intertidal and subtidal habitat selection by the Rock Gunnel along the US East Coast. To quantify characteristics of intertidal microhabitats and their usage by the Rock Gunnel, we conducted intertidal quadrat surveys in midcoast Maine and New Brunswick. Using datasets from trawl surveys conducted by state (Massachusetts and Connecticut) and federal fishery management agencies, we investigated how subtidal habitat characteristics influenced the occurrence of Rock Gunnel in trawl yields. Logistic regression and classification and regression tree (CART) analysis showed that Rock Gunnels preferred microhabitats in the lower intertidal zone, with sand/pebble/gravel substrata and overlying cobbles, tidepools, and dense algal cover. The occurrence of Rock Gunnel in trawl yields did not depend upon temperature, salinity, or latitude, but decreased with depth and increased moving eastward. In the intertidal zone, the Rock Gunnel appears to select habitat that minimizes the risks of predation and desiccation at low tide, while allowing access to abundant intertidal prey resources at high tide. The Rock Gunnel's broad physiological tolerances suggest that its selection of habitat in the subtidal zone is driven primarily by the availability of sheltering structure and biotic factors, rather than by temperature or salinity.