The composition of the fatty acids (FAs) of the particulate matter (size fraction 0.2-100 mu m) in five ponds of increasing salinity in the Sfax solar saltern (Tunisia) was Studied simultaneously With the abundance of bacteria pico-nano-microphytoplankton and ciliates during the winter of 2006. The FAs analysis was performed by gas chromatography and gas chromatography coupled with mass spectrometry. The potential relationships between FAs and micro-organisms were tested through redundancy analysis (RDA) which allowed to keep all physico-chemical factors constant, including salinity. The results showed a great diversity of FAs from 10 to 24 carbon atoms, which Could be saturated, unsaturated, linear or branched. The predominant saturated FAs were 14:0, 16:0 and 18:0, and might originate from diatoms, Dinophyceae and flagellates for the first ponds and from Chlorophyceae, heterotrophic bacteria (HB) in hypersaline ponds. The polyunsaturated fatty acids (PUFAs) (EPA: eicosapentaenoic acid, DHA: docosahexaenoic acid) were detected in small quantities. The branched fatty acids (18:0 12Me or 18:2 12Me) might be attributed primarily to bacteria and archea. Species richness and abundance of aquatic microorganisms decreased as the salt concentration increased, while dominant FAs profiles were overall similar along the salinity gradient.