Viruses of bacteria are ubiquitous in most ecosystems, have essential roles in biogeochemical cycling and may cause ripple effects in higher trophic levels of food webs. Though much progress has been made in charting virus diversity and ecology in natural systems, little is known about how the observed biogeographical patterns of viruses came to exist, beyond abiotic pressures. Niche establishment and/or expansion via strain generation in the context of virus-host interactions is thought to involve genomic islands (GIs)— regions of high diversity that could reflect rapid evolutionary adaptation to biotic pressures. In mixed metagenomic assemblies, GIs can be missed due to high sequence variability. However, long-read viromics is a promising approach to detect them. Here, we generated long-read-augmented viromes from seawater and soil samples and detected hundreds more GIs in hybrid assemblies compared to short-read assemblies.