The occurrence and spread of antibiotic resistant bacteria and antibiotic resistant genes have become an important environmental contamination issue worldwide. We investigated the occurrence and diversity of indigenous microbial communities carrying antibiotic resistance genes in an aquifer recharged with urban groundwater. Microcosms with silica wool were placed at a depth of 170m to capture the flow of injected storm water and encourage biofilm development. Biofilm samples were collected after 1, 2 and 3 months of incubation. Extracted DNA from the biofilms was subjected to DNA microarray analysis (Geochip 4.2) containing probes targeting unique sequences to analyse microbial diversity, composition and antibiotic resistance genes, β-lactamase A, B and C. In general, β-lactamase A, and C genes were more frequently detected and genes were derived from 38 and 75 genera, respectively. Whereas, only β-lactamase B genes were derived from bacteria belonging to the Bacillus and Leptospira genera were detected. The β-lactamase A gene derived from the genera Burkholderia, Erythrobacter, Mycobacterium and Yersisnia was more frequently detected. Whereas, the β-lactamase C gene derived from members of the genera Enterobacter, Yersisnia, Pseudomonas, Spirosoma, Mycobacterium, and Halogeometricum was more frequently detected.