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Flood-induced disturbance causes major shifts in the diversity and function of microbial communities in desert streams. We compared bacterial community structure (using automated rRNA intergenic spacer analysis, ARISA), pigment composition and nitrogen fixation rates in benthic microbial mats from stone surfaces collected from 6 sites along a desert stream in the Sultanate of Oman before and 2 wk after an intense flood. Flooding caused partial flushing out of old mats, and new mats re-established on the surfaces of rocks. Visually, the filamentous green algae Spirogyra spp. in creased in abundance in the water column at most sites after the flood, and direct microscopy revealed that the newly developed mats were dominated by the heterocystous Calothrix spp. Multivariate analyses of ARISA profiles revealed that, in each mat, the structure of the bacterial community was different after the flood (analysis of similarities [ANOSIM], R = 0.49, p < 0.001), and pairwise comparison of the presence/absence of operational taxonomic units (OTUs) showed that only between 18 and 26% shared OTUs. The OTU richness in the newly developed microbial communities decreased in 6 mats after the flood, but remained similar or slightly increased in the other 6 mats. Out of the 9 detected pigments, chlorophyll a, scytonemin, fucoxanthin, diadinoxanthin and beta-carotene showed site-specific changes with flooding. The average acetylene reduction rates increased after the flood at all sites; however, this increase was statistically significant at only 2 sites due to the high variance among samples. In conclusion, flooding resulted in the replacement of over 74% of the microbial communities within mats, while nitrogen fixation rates remained stable or increased.