This study aimed to reveal microbial populations in Chinese raw milk using both 16S rRNA sequencing and high-throughput sequence (HTS) methods. Psychrotrophic isolates were clustered into 23 genera and 57 species, and the abundant genera in raw milk were Pseudomonas, Acinetobacter and Lactococcus. Genetic diversity and biofilm-forming capacity of Pseudomonas isolates were analysed using random amplified polymorphic DNA (RAPD) and crystal violet staining assay, respectively. Heterogeneous biofilm-forming ability of Pseudomonas isolates with the same RAPD patterns was observed. HTS analysis revealed a 33-fold higher diversity at the genus level, and a different bacterial population was predominated by Flavobacterium, Pseudomonas and Acinetobacter. The results provide insight into the microbial contamination of raw milk.