Abstract: Orchid entophytic bacteria and mycorrhizal fungi grown in collaboration can have a positive effect on host plants in terms of disease resistance, stress tolerance and phytoremediation. Understanding the endogenous relationship between bacterial diversity and habitat can reveal the adaptation and evolution mechanisms of orchid plants. The endogenous bacterial diversity and spatial heterogeneity in different habitats of Phalaenopsis pulcherrima, an endemic Southeast Asian orchid species, were analysed by molecular techniques. Fifty-nine strains of entophytic bacteria were isolated from the roots of P. pulcherrima in different habitats, including forty-five (76.27%) and fourteen (23.73%) strains of entophytic bacteria isolated from land-borne and stone-borne type populations, respectively. Based on 16S rDNA sequence analysis, fifty-nine strains of entophytic bacteria isolated from P. pulcherrima were classified into seven genera, that was, Bacillus, Burkholderia, Pandoraea, Agrobacterium, Paenibacillus, Pantoea, and Erwinia. Among the entophytic bacterial strains, Bacillus was the dominant genus, followed by Pantoea and Burkholderia. The diversity index of land-borne type populations was greater than that of stone-borne type populations. Analysis of molecular variance (AMOVA) also showed that the entophytic bacterial community structures of P. pulcherrima in distinct habitats were significantly different (P < 0.01), with land-type dominant species found in Bacillus and Pantoea, and stone-type dominant species found in Bacillus and Burkholderia.