These data describe habitat associations of juvenile parrotfish (Scaridae) encountered during systematic searches at LTER 1 and LTER 2 fringing reef and back reef sites during March 2011. At each site SCUBA divers or snorkelers identified, counted, and estimated the sizes of juvenile parrotfish and recorded the microhabitat that each individual or group of individuals was associated with on two 100 m x 10 m wide transects (n = 8 transects total). Upon encountering a juvenile or group of juveniles, the surveyor recorded the microhabitat type that fishes were first seen to be closest to. They also closely observed the behavior of fishes to see if they were utilizing a particular microhabitat as shelter, and if so this was also recorded. Several groups of fishes first observed to be grazing on hard substrate or on macroalgae quickly retreated into the nearby coral Porites rus when approached. Hence for these individuals we considered the initial habitat they were associated with (e.g., hard substrate or macroalgae) to be their primary microhabitat, but also noted that they were associated with Porites rus for shelter.