Two methods of floor cleaning (dry and wet) are employed in railway station restrooms in Japan dependent on the type of flooring. To date, research characterizing floor microbiomes is scarce. In this study, the microbiomes of men's restroom floors in two railway stations subject to different cleaning methods were analyzed. The microbiomes of dry‐cleaned restroom floors were similar from one sampling location to another prior to cleaning. The microbiomes of five sampling points on the floor before and after cleaning were significantly different. Paracoccus, Staphylococcus, Corynebacterium, and Rickettsiella were characteristic genera before cleaning, and Cellvibrio, Salinicoccus, and Asticcacaulis were characteristic after cleaning. The microbiomes of wet‐cleaned restroom floors differed among sampling points prior to cleaning. The microbiomes of five sampling points on the floor before and after cleaning were not significantly different. Anaerococcus and Pseudomonas were the characteristics before and after cleaning genera, respectively. Analysis of the airborne microbiomes inside and outside the men's restrooms revealed that Kocuria, Pseudomonas, and Cellvibrio, which were the dominant genera on the floor following dry cleaning, and Pseudomonas, which were the dominant genera on the floor following a wet cleaning, were detected in the air inside the respective restrooms following cleaning.