Cyanobacterial mats are common in Antarctic lakes, ponds and on moist soils. The species comprising these mats have adapted to tolerate extreme conditions (e.g. high salinities and UV radiation, freezing and extended periods of darkness). In this study, cyanobacterial mats were collected from shallow melt-water ponds in Pyramid Trough in Southern Victoria Land, Antarctica. Eight strains were isolated and characterised by morphological and molecular (16S rRNA gene sequences) techniques and their fatty acid methyl ester (FAME) and lipid class profiles determined. These data were compared to parallel information obtained from cyanobacterial cultures isolated from New Zealand. In general, the morphological and molecular characterisation complemented each other, and the Antarctic strains identified belonged to the orders: Oscillatoriales (six), Nostocales (one) and Chroococcales (one). Two of the Antarctic strains (CYN67 and CYN68) showed low similarity (<96% 16S rRNA gene sequence) when compared to other cultured cyanobacteria. The fatty acid (FA) profiles from the Antarctic and New Zealand strains shared many similarities with palmitic (C16:0), stearic (C18:0) and oleic acid (C18:1n-9) most abundant. In contrast, the lipid class analysis differed among geographic locations with Antarctic strains containing higher amounts of hydrocarbons and eicosapentaenoic and hexadecatrienoic acids.