The dramatic increase in obesity and associated diseases has focused interest on the influence of dietary ingredients in controlling satiety. Dietary resistant starch (RS) undergoes colonic microbial fermentation leading to increased short-chain fatty acid (SCFA) concentrations, which may increase satiety via the SCFA-induced release of gastrointestinal hormones such as glucagon-like peptide-1 and polypeptide YY. This work utilised high-throughput 16S rDNA sequencing to characterise changes occurring in the intestinal microbiota following incorporation of a novel type III RS into the diet. This approach provided a more in-depth and comprehensive analysis than previous qPCR, 454 and microarray-based studies. All subjects (n=22) followed a controlled 44-day crossover dietary plan. Faecal samples were collected during each of the four diets: maintenance (3d), weight-loss (21d), control (10d) and RS type III (C*ActiStar 11700, Cargill) (10d). Extracted microbial 16S rDNA was then sequenced using the Illumina MiSeq platform and analyses were generated using QIIME and Metastats software. To understand how RS affected the faecal microbiota, only samples from the control and RS diets were incorporated into the statistical analyses. The inclusion of RS into the diet significantly changed the faecal microbiota by altering the abundance of selective groups of diet-responsive taxa (p<0.05, ADONIS, weighted Unifrac). Phylogenetic diversity (PD) did not change following the consumption of RS, indicating that microbial changes were related to abundance rather than incidence (presence/absence) (p>0.05, nonparametric t-test, PD). At the genus level, Roseburia, Ruminococcus and Faecalibacterium were significantly higher following RS consumption, exhibiting average fold increases of 1.5, 1.4 and 1.2 respectively (p<0.05, Metastats). The increased abundance of both Ruminococcus and Roseburia was largely attributable to changes in R. bromii and an unclassified Roseburia species (p<0.05, Metastats). R. bromii and relatives of Roseburia have previously been correlated with increased consumption of an RS type III, however the specific increase in Faecalibacterium has not been observed before. Here, using a whole-community approach, we show that three genera which have been associated with either SCFA synthesis and/or starch degradation, are significantly enriched by the consumption of this novel RS. Moreover, these data demonstrate the selective enrichment of a distinct number of “key” species in response to addition of this RS into the diet, possibly due to substrate-specificity at the species level.