The lipid composition of microalgal communities dominated by diatoms collected from the sea ice at three locations within McMurdo Sound during the austral spring bloom of 1989/90, was determined using gas chromatography (GC) and GC mass spectrometry. A range of C27-C29 sterols were detected. The major sterols found at the three sites were 24-methylcholesta-5, 22E-diene-3β-ol (Cape Armitage); trans-22-dehydrocholesterol, 24-ethylcholesterol and 24-methylenecholesta (Erebus Ice Tongue); and 24-methylenecholesterol (Cape Royds). The difference in sterol profiles is believed to reflect the differing species composition at each site. The high relative levels (as % of total) of 24-ethylcholesterol at the Erebus Ice Tongue site (possibly related to Amphiprora kufferathii) supports the proposal that diatoms are a more probable source of C29 sterols in Antarctic lakes than are other algal groups or cyanobacteria. Changes in sterol composition over the course of the bloom were evident at the Cape Armitage site, particularly within the cellular free-lipid fraction. The major fatty acids identified were 14:0, 16:0, 16:1ω7c, 16:4ω1 and 20:5ω3 (Cape Armitage and Erebus Ice tongue sites); 16:0, 16:1ω7c and 20:5ω3 (Cape Royds site). All sites demonstrated high levels of PUFA (40–50% of total fatty acids), with an average 20:5ω3 level of 21% Erebus Ice Tongue, 20% Cape Royds, and 17% Cape Armitage. Variation was also observed in the percentage of 20:5ω3 for the Cape Armitage community over the sampling period. Levels of 22:6ω3 were between 0.4 and 1% of total fatty acids for the three sites. A C25:2 isoprenoid hydrocarbon was present in samples from all sites, adding further evidence to the proposal that diatoms are probably a source of this and related isoprenoid alkenes in marine and coastal sediments.