Temporal variation in soil microbial communities was studied at a mid-alpine environment in Latnjajaure, northern Sweden, using phospholipid fatty acid (PLFA) analysis. The results show two seasonal shifts in microbial composition. The first shift was associated with snowmelt and mainly related to a decrease in fungal PLFAs, accompanied by an increase in branched 17:0 and methylated PLFAs (biomarkers for Gram-positive- and actinobacteria, respectively), resulting in a decrease in the ratio of fungi-to-bacteria. The second shift occurred across the growing season, and was associated with a switch from shorter to longer PLFAs and an increase in 18:1ω7 (biomarker for Gram-negative bacteria). Vegetation, snow cover dynamics, and N turnover seem to be of minor importance to broad-scale microbial community structure in this area.