Arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria (NFB) are critical to plant growth and recovery in degraded ecosystems. However, information about the relationships between these microorganisms in the rhizosphere soils of natural ecosystems is limited. Rhizosphere soils from six common plant species: (Loropetalum chinense, Syzygium championii, Alchornea trewioides, Bauhinia purpurea, Pterolobium punctatum and Albizia odoratissima), were sampled in the karst region of Southwest China. The abundance and community composition of AM fungi and NFB were measured using quantitative polymerase chain reaction (qPCR) and terminal restriction fragment length polymorphism (T-RFLP). The community composition and abundance of AM fungi and NFB varied among plant rhizosphere soils, but the richness of these microbes was not significantly different. The abundances of AM fungi and NFB significantly related to each other. Specifically, dominant 278-bp and 105-bp terminal restriction fragments (T-RFs) of AM fungi positively linked with dominant 184-bp and 180-bp T-RFs of NFB (P<0.05), respectively. Redundant analyses indicated that soil organic carbon, available phosphorus, and total nitrogen significantly correlated with the composition of fungal and bacterial communities. These results suggest that AM fungi and NFB have host-plant specificity and that these microbes are closely linked in plant rhizosphere soils of the karst region.