Although Cladophora species frequently appear in brackish environments, their genetic diversity, phenological patterns and physiological properties have not been well investigated in these environments. Cladophora is distributed throughout Mikata-goko, an area consisting of five coastal lakes that are directly or indirectly connected to the sea, resulting in a salinity gradient ranging from fully marine to freshwater. To elucidate genetic and ecological variation in Cladophora, we monthly compared ribosomal internal transcribed spacer sequences of Cladophora specimens across six study sites characterized by different salinity regimes for a year. A total of 12 ribotypes were detected and assigned to six species, four of which were restricted to the marine habitat. Ribotype I of C. vagabunda (L.) Hoek was distributed in high-salinity brackish waters (mean salinity ≤13 psu; maximum salinity ≤31 psu), whereas C. vagabunda ribotype II and C. glomerata were abundant in low-salinity brackish waters (mean salinity ≤5 psu; maximum salinity ≤10 psu). Although Cladophora albida (Nees) Kütz. and C. glomerata (L.) Kütz. were collected during all four seasons, C. laetevirens (Dillwyn) Kütz., C. oligocladoidea Hoek and Chihara, C. opaca Sakai and C. vagabunda displayed marked seasonal variation. Culture experiments revealed that optimal salinity conditions for vegetative growth vary among ribotypes collected from different salinity regimes, suggesting that Cladophora distributions are controlled by ribotype-specific ecophysiological adaptations. In contrast, temperature optima and tolerance were similar among ribotypes showing different seasonalities, and thus their phenologies may be controlled by other environmental factors or biotic conditions, such as reproductive maturity and spore germination.