Patterns of nine intracellular free amino acids (FAA), which are utilized as organic osmolytes for salinity-induced cell volume regulation in marine osmoconformers, were compared in five Macoma balthica populations and seven Mytilus spp. populations along their European distribution. Three types of FAA patterns were classified within both taxa: a northern Baltic type, a southern Baltic type and an Atlantic/Mediterranean type which mainly differ regarding the share of alanine and taurine. Differences are discussed in relation to habitat salinity and population genetics. Along a salinity gradient, the total size of the intracellular FAA pool did not differ between sympatric M. balthica and Mytilus spp., and was significantly correlated with habitat osmolality in a range from 70 to 600 mmol kg−1 H2O (oligohaline to mesohaline) in both bivalves. In M. balthica, this correlation was mainly based on significant correlations of alanine (15–100 mmol kg−1 DW), glycine (30–100 mmol kg−1 DW) and taurine (0–70 mmol kg−1 DW) with habitat osmolality. In Mytilus spp., only glycine (25–100 mmol kg−1 DW) and taurine (4–180 mmol kg−1 DW) were significantly correlated with habitat osmolality. The concentration of alanine was three times lower in Mytilus spp. than in M. balthica and did not correlate with habitat osmolality. Within a habitat osmolality range from 600 to 1,100 mmol kg−1 H2O (mesohaline to marine) the concentration of FAA remained constant in both taxa. It is suggested that under marine conditions additional organic osmolytes must become more important for cell volume regulation in Macoma and Mytilus.