While the microbiome in indoor environments such as hospitals has drawn increasing attention, the transmission routes especially for pathogens in ICUs remain largely unexamined. In this study, we have explored the distinct bacterial communities of ICU compared with Non-ICU in hospital wards. We have then clarified their different transmission patterns by means of microbial source tracking, with results suggesting that bedrail and inside floor were hubs in two wards, respectively. Streptococcus , Staphylococcus were identified as “Transfer-Easy taxa” that were found in both ICU and Non-ICU settings, with potential pathogenicity and cases recorded. We have also detected another 15 pathogenic genera in hospital environment, including Pseudomonas and Acinetobacter , and charted how these pathogenic microorganisms affect patients, demonstrating that there were far more strong routes for pathogens transmitted from environment to patients in ICU. In summary, this work investigates patterns of bacterial transmission in hospital settings, highlights pathogenic genera that are likely to transfer from the environment to humans and cause nosocomial infection, which could provide guidance for healthcare system monitoring and co-infection avoidance. • Microbial community patterns and transmission routes differ between ICU and non-ICU wards. • Several genera with strong transmission capacity could transfer from the outside environment to patients. • A group of pathogens discovered in ICU wards indicate a high probability of co-infection.