Summary We explored the association between gut microbiota composition and bone mineral loss in Chinese elderly people by high-throughput 16S ribosomal RNA (rRNA) gene sequencing. Compared with controls, a smaller number of operational taxonomic units (OTUs), several taxa with altered abundance, and specific functional pathways were found in individuals with low-bone mineral density (BMD). Introduction Gut microbiota plays important roles in human health and associates with a number of diseases. However, few studies explored its association with bone mineral loss in human. Methods We collected 102 fecal samples from each eligible individual belonging to low-BMD and control groups for high-throughput 16S rRNA gene sequencing. Results The low-BMD individuals had a smaller number of OTUs and bacterial taxa at each level. At the phylum level, Bacteroidetes were more abundant in the low-BMD group; Firmicutes were enriched in the control group; Firmicutes and Actinobacteria positively correlated and Bacteroidetes negatively correlated with the BMD and T-score in all subjects. At the family level, the abundance of Lachnospiraceae in low-BMD individuals reduced and positively correlated with BMD and T-score; meanwhile, BMD increased with increasing Bifidobacteriaceae. At the genus level, low-BMD individuals had decreased proportions of Roseburia compared with control ones ( P  < 0.05). Roseburia , Bifidobacterium , and Lactobacillus positively correlated with BMD and T-score. Furthermore, BMD increased with rising abundance of Bifidobacterium . Functional prediction revealed that 93 metabolic pathways significantly differed between the two groups (FDR-corrected P  < 0.05). Most pathways, especially pathways related to LPS biosynthesis, were more abundant in low-BMD individuals than in control ones. Conclusions Several taxa with altered abundance and specific functional pathways were discovered in low-BMD individuals. Our findings provide novel epidemiologic evidence to elucidate the underlying microbiota-relevant mechanism in bone mineral loss and osteoporosis.