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The effect of environmental conditions; and especially soil water content, on microbial community structure was quantified during a 15-month sampling period (1994-1995) in a Negev Desert soil system by determination of phospholipid fatty acids (PLFAs). Two rainy seasons were observed during the study period: (1) the rainy season of 1993-1994, with a total rainfall of 58 mm, and (2) the rainy season of 1994-1995, with a total of 140 nun, which is 55% more than the multiannual average. Soil samples collected from the 0-10 cm layer exhibited changes in soil moisture and PLFA composition. Palmitic acid (nC16:0) was found to be the most common acid, with a maximum abundance found in May 1994 (27.2%). Oleic acid (C18: 1w9) was found to be the second highest in abundance, with high levels in January 1994 (14%), decreasing gradually to 1.3% of total ion current in January 1995. This decrease was interpreted as being caused by abiotic factors affecting the microbial community, resulting in fatty acid profile and lipid abundance. Other acids were found to be present in relatively small amounts. The iC17:1w9 and C18:2w8,11 were found among the major PLFAs during the study period. Thedata obtained in this study were found to be similar to data obtained in soils of temperate climates, in spite of the hypothesis that the total PLFAs of the desert soil microbes are triggered and depend on soil Hater availability. This can afford special data interpretation of the viable biomass of the soil microbes and their metabolic status.