ABSTRACTModels of the diatom associations found in upper Florida Bay and adjoining sounds have been constructed utilizing Q modal factor‐vector analysis and ecologic diversity indices (Shannon index, number of species, evenness). Four distinct associations were defined using Q‐mode factor‐vector analysis. Two associations were epiphytic, occurring onThalassia testudinumKönig—Association I was characterized byCocconeis placentulaEhr., Association III byCylindrotheca closterium(Ehr.) Reim.&Lewin andCocconeis placentulaEhr. The other two associations were epipelic, occurring on the carbonate mud substratum—Association II was characterized byCyclotella striata(Kütz.) Grun.,Rhopalodia gibberula(Ehr.) O. Müller andSurirella fastuosa(Ehr.) Kütz., Association IV byFragilaria crotonensisKitton andCyclotella striata(Kütz.) Grun. The majority of the 161 species identified were present in both the epiphytic and epipelic assemblages. Only 33 species were restricted to the epiphyton, and 18 species restricted to the epipelon. The epipelic assemblage was significantly more diverse than was the epiphytic assemblage. A general trend of increased diversity away from terrestrial environs toward more open areas of water in both the epipelon and epiphyton