The composition and functional capacity of the microbial communities on microplastics, especially in the smaller size range (<1 mm), have largely been unexplored. As microplastic is a relatively newly discovered pollutant, sampling technique has not been well-established for the marine environment and is especially arduous due to equipment material incompatibility. The difficulty level increases when the microbial aspect should be considered in the sampling. Earlier studies have typically sampled microplastics either using manta-trawling or pumping water through a cascade of sieves, while collecting the microbiological samples separately either pre- or post- microplastic sampling. To simultaneously capture microplastic and microbial community from discrete samples, we developed an integrated and rapid sampling method using an in-house designed microplastic surface sampler, a series of filter cartridges, and a OSMO autosampler. A Proactive Mini-Typhoon pump is attached to the surface sampler and pumps water through a series of stainless-steel filter cartridges with mesh sizes 300, 100 and 20 µm. The output from the filter cartridges is then channelled into a peristaltic pump to sample for bacterial analysis on Sterivex filters simultaneously. This method allows for the collection of microplastics and bacteria from different depths without interferences from waves and vertical mixing. It is also able to support the collection of large water volumes, which is necessary for reliable quantification of microplastics and associated microbiome. With this sampling technique, marine microplastics and its associated microbial composition are determined for the Southeast Asia region to understand the role of microplastics as vector for pathogens.