To compile reference data for palaeolimnological studies using fossil pigments, we examined the extent to which environmental variables, gross morphology and species composition influence the modern pigment content of in situ microbial communities in 62 east Antarctic lakes. Pigment contents, measured using HPLC, were compared with 32 environmental variables, gross microbial mat morphology and cyanobacterial species composition in each lake. Results showed low concentrations or an absence of pigments in the water columns of most lakes. For benthic microbial communities, multivariate statistical analyses identified lake depth as the most important factor explaining pigment composition. In deeper lakes the pigment composition was dominated by chlorophylls, in intermediate depth lakes by chlorophylls and carotenoids, and in shallow lakes by scytonemins, ultraviolet-screening pigments found in cyanobacteria. In addition to lake depth, conductivity, turbidity, dissolved oxygen, sulphate and geographical location were all significant (p less than or equal to 0.05) in explaining variance in the pigment content. Significant differences in microbial mat gross morphologies occurred at different lake depths (p less than or equal to 0.01), and were characterised by significant differences in their pigment content (p less than or equal to 0.004). Despite the high abundance of scytonemin in shallow lakes, there were only limited changes in the absolute concentrations of chlorophylls and carotenoids. We conclude that lake depth is the most significant factor influencing both gross mat morphology and pigment content, presumably as a result of its influence on the light climate. In general, the ability of the cyanobacteria to regulate their pigment content, morphology, community composition and motility to best exploit the light environment at different lake depths may explain their dominance in these systems.