Being integral primary producers in diverse ecosystems, microalgal genomes could be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar and cellular membrane functions. Further, marine species contained significantly more viral families in their genomes (p = 8e–4). Sequences from Chlorovirus, Coccolithovirus, Pandoravirus, Marseillevirus, Tupanvirus, and other viruses were found integrated into the genomes of algal from marine environments. These viral-origin sequences were found to be expressed and code for a wide variety of functions. Together, this study comprehensively defines the expanse of protein-coding and viral elements in microalgal genomes and posits a unified adaptive strategy for algal halotolerance. Display omitted •107 microalgae from diverse phlya and environments were cultured and sequenced•Membrane-related protein families were significantly enriched in saltwater species•Nuclear-related protein families were significantly enriched in freshwater species•More than 90,000 viral-origin sequences in 184 algal genomes were discovered Nelson et al. combine high-throughput cultivation, genome sequencing, and bioinformatics strategies to generate resources for gaining new perspectives on microalgae from diverse lineages and environments. This resource greatly expands the available collection of algal genomes and provides insight into how viral sequence integration shaped major algal clades.