Phthalate monoesters (me-PAEs) have been used as biomarkers for assessing human exposure to phthalate esters (PAEs) for a long time, and studies on the sources and distribution of me-PAEs in the environment are limited. In this study, dust samples from microenvironments were collected to measure the occurrence of PAEs and me-PAEs, as well as the bacterial diversity. The results indicated that me-PAEs coexisted with PAEs in different microenvironmental dust samples, with concentrations of nine PAEs and 16 me-PAEs ranging from 108 to 1450 μg/g (median range) and 6.00 to 21.6 μg/g, respectively. The concentrations of several low molecular weight me-PAEs (e.g., monomethyl phthalate and monoethyl phthalate) in dust were even significantly higher than those of their parents. The bacteria in the dust were mainly predominant with Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes (total abundance >90%). Bacteria from bus and air conditioning dust samples had the highest species richness and species diversity. Seven genes of suspected enzymes with the ability to degrade PAEs were selected, and the concentration of me-PAEs increased with increasing abundance of enzyme function. Our findings will provide useful information on the profiles of me-PAEs and their potential sources in indoor dusts, which will benefit the accurate estimation of human exposure.