The knowledge regarding the intestinal microbial types involved in isoflavone bioavailability and metabolism is still limited. The present work reports the influence of a treatment with isoflavones for 6 months on the fecal bacterial communities of 16 menopausal women, as determined by culturing and culture-independent microbial techniques. Changes in fecal communities were analyzed with respect to the women's equol-producing phenotype. Compared to baseline, at 1 and 3 months the counts for all microbial populations in the feces of equol-producing women had increased strongly. In contrast, among the non-producers, the counts for all microbial populations at 1 month were similar to those at baseline, and decreased significantly by 3 and 6 months. Following isoflavone intake, major bands in the denaturing gradient gel electrophoresis (DGGE) profiles appeared and disappeared, suggesting important changes in majority populations. In some women, increases were seen in the intensity of specific DGGE bands corresponding to microorganisms known to be involved in the metabolism of dietary phytoestrogens (Lactonifactor longoviformis, Faecalibacterium prausnitzii, Bifidobacterium sp., Ruminococcus sp.). Real-Time quantitative PCR revealed that the Clostridium leptum and C. coccoides populations increased in equol producers, while those of bifidobacteria and enterobacteria decreased, and vice versa in the non-producers. Finally, the Atopobium population increased in both groups, but especially in the non-producers at three months. As the main findings of this study, (i) variations in the microbial communities over the 6-month period of isoflavone supplementation were large; (ii) no changes in the fecal microbial populations that were convincingly treatment-specific were seen; and (iii) the production of equol did not appear to be associated with the presence of, or increase in the population of, any of the majority bacterial types analyzed.