The antibiotic resistance issue in low- and middle-income countries has drawn global concern. This study presents the first metagenomic investigation of antibiotic resistance genes (ARGs) in hospital and municipal wastewater treatment plants (WWTPs) in Sri Lanka, using Illumina short-read and Nanopore long-read sequencing. Samples from three representative WWTPs receiving hospital and/or municipal wastewater (domestic generated) were collected from four districts in Sri Lanka, and as a comparison, wastewater directly discharged without treatment was also taken. ARG abundance was significantly higher in hospital wastewater (7.22 copies/cell) than in municipal wastewater (2.33 copies/cell), and greatly decreased by 82 % and 93 % after treatment processes, respectively. Similar trends were observed for mobile genetic elements. The prevalent subtypes of clinically relevant extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater were blaOXA, blaGES, blaVEB and blaTEM, whereas blaCTX-M and blaNDM were less dominant, which indicated the potential unique distribution pattern of ESBL and carbapenemase genes in Sri Lanka. Using long-read metagenomics, bacterial host range and genetic locations (plasmid or chromosome) of ARGs in sludge samples were predicted. Diverse pathogenic host taxa (Pseudomonas, Streptococcus, Salmonella and Escherichia) and a higher plasmid proportion were identified in the hospital WWTP (39.8 % vs. 21.5 % in the municipal WWTP). Detected mobile genetic contexts in this study, IS6100-sul1-blaOXA-329-blaGES-5-blaGES-5-intI1 and ISKpn6-blaKPC-2-ISKpn7-ISPsy42, were also common in antibiotic-resistant plasmids in Enterobacteriaceae from different countries. These data will serve to expand the inventory of global ARG epidemiology. Also, the finding emphasizes that the wastewater treatment projects, especially in healthcare facilities, are vital for reducing clinically relevant ARG discharge to the environment. Further monitoring using advanced meta-omics approaches is crucial to assess potential ARG risks and optimize control strategies for improving human and ecosystem health in Sri Lanka.