Shotgun whole metagenome sequencing (WMS) of 27 soil samples from rooftop and surface gardens in Dhaka and Gazipur yielded 1.34 billion reads (avg. 49.8M/sample), with 27.8M high-quality reads (2.1%) mapped to 766 OTUs. A total of 19 phyla, 31 classes, 75 orders, 122 families, 275 genera, and 755 species were identified.