The effects of the herbicide Roundup (R) (glyphosate) on natural marine microbial communities were assessed in a 7-day field experiment using microcosms. Bottles were maintained underwater at 6 m depth, and 10% of their water content was changed every other day. The comparison of control microcosms and surrounding surface water showed that the microcosm system tested here can be considered as representative of the natural surrounding environment. A temporal temperature gradient gel electrophoresis (TTGE) was run on 165 and 18S rDNA-amplified extracts from the whole microbial community. Cluster analysis of the 16S gel showed differences between control and treatment fingerprints for Roundup at 1 mu g L-1 (ANOSIM,p=0.055; R=0.53), and 10 mu g L-1 (ANOSIM, p=0.086; R=0.40). Flow cytometry analysis revealed a significant increase in the prasinophyte-like population when Roundup concentration was increased to 10 mu g L-1. This study demonstrates that a disturbance was caused to the marine microbial community exposed to 1 mu g L-1 Roundup concentration, a value typical of those reported in coastal waters during a run-off event. (C) 2008 Elsevier B.V. All rights reserved.