SUMMARY. An ecological study of two small maritime Antarctic lakes on Signy Island, South Orkney Islands, was undertaken from January 1986 to March 1987. Analysis of diatom counts from the lakes provided examples of oligotrophic and mesotrophic ecosystems. A diverse community of 104 epiphytic taxa was identified. Twenty‐eight taxa had a percentage abundance greater than 1% in both lakes. Distinctive dominant taxa were identified from each lake. A variety of ordination techniques was performed on the abundance data and a principal components analysis demonstrated differences in the diatom assemblages between the two lakes. Clear separations of sites and species were evident between the lakes, and accounted for the greatest percentage variance. Species composition varied with depth within each lake and was also important in influencing changes in assemblage composition between sites. A redundancy analysis indicated that species composition was correlated to concentrations of nitrogen and phosphorus but the total variance accounted for by the four physical and chemical factors measured was low (24%).