Species of Ulva (Ulvaceae, Chlorophyta) are relatively common macroalgae in most coastal areas. In this paper, we examine Ulva in inland aquatic ecosystems to determine relationships between the chemical parameters of the water and the Ulva taxa present. Two groups of samples of freshwater Ulva were selected from: (i) habitats with high salinity levels, and (ii) habitats with fresh or slightly saline waters. We showed that these two groups of Ulva, which occupy distinct habitats, represent two separate taxa. The first group represents Ulva flexuosa subsp. pilifera (Kützing) M.J. Wynne, which is very common and regularly encountered in fresh waters, but is equally well represented in slightly saline waters. The second is U. flexuosa subsp. paradoxa (C. Agardh) M.J. Wynne, which is less common, preferring mainly salt-wedge saline waters. We did not find both Ulva flexuosa subspecies together at any of the research sites.There were significant morphological differences between the Ulva flexuosa subspecies. Ulva flexuosa subsp. pilifera had longer and wider thalli and wider cells than those of subsp. paradoxa. Ulva flexuosa subsp. paradoxa cells were longer and of greater circumference than those of subsp. pilifera. Analyses of the rRNA ITS region and partial rbcL gene sequences demonstrated minor sequence variation within the two subspecies. The results of this study provide detailed information on the characteristics of limnic Ulva habitats and indicate the niches where such populations are likely to occur.