The Florida Everglades is a mosaic of short and long-hydroperiod marshes that differ in the depth, duration, and timing of inundation. Algae are important primary producers in widespread Everglades' periphyton mats, but relationships of algal production and community structure to hydrologic variability are poorly understood. We quantified differences in algal biomass and community structure between periphyton mats in 5 short and 6 long-hydroperiod marshes in Everglades National Park (ENP) in October 2000. We related differences to water depth and total phosphorus (TP) concentration in the water, periphyton and soils. Long and short-hydroperiod marshes differed in water depth (73 cm vs. 13 cm), periphyton TP concentrations (172 lg g )1 vs. 107 lg g )1 , respectively) and soil TP (284 lg g )1 vs. 145 lg g )1 ). Periphyton was abundant in both marshes, with short-hydroperiod sites having greater biomass than long-hydroperiod sites (2936 vs. 575 grams ash-free dry mass m )2 ). A total of 156 algal taxa were identified and separated into diatom (68 species from 21 genera) and ''soft algae'' (88 non-diatom species from 47 genera) categories for further analyses. Although diatom total abundance was greater in long-hydroperiod mats, diatom species richness was significantly greater in short-hydroperiod periphyton mats (62 vs. 47 diatom taxa). Soft algal species richness was greater in long-hydroperiod sites (81 vs. 67 soft algae taxa). Relative abundances of individual taxa were significantly different among the two site types, with soft algal distributions being driven by water depth, and diatom distributions by water depth and TP concentration in the water and periphyton. Periphyton communities differ between short and long-hydroperiod marshes, but because they share many taxa, alterations in hydroperiod could rapidly promote the alternate community.