The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats in temperate, subtropical, and tropical seas. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb and a scaffold N50 of 108.93 Mb. Approximately 93.81% of contigs were anchored onto 22 chromosomes. Phylogenetically, D. delphis was located close to Tursiops truncatus and T. aduncus, and exhibited high synteny with T. truncatus. The genome of D. delphis exhibited 428 expanded and 1,885 contracted gene families, and 120 genes were identified as positively selected. The expansion of the HSP70 gene family indicated that D. delphis has a powerful system for buffering stress, which might be associated with its broad adaptability, longevity, and detoxification capacity. The expanded IFN-α and IFN-ω gene families, as well as the positively selected genes encoding tripartite motif-containing protein 25, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, and p38 MAP kinase, were all involved in pathways for antiviral, anti-inflammatory, and antineoplastic mechanisms in D. delphis. The genome data also revealed dramatic fluctuations in the effective population size of D. delphis during the Pleistocene. Overall, the high-quality genome assembly and annotation represent significant molecular resources for ecological and evolutionary studies of Delphinus and help support their sustainable treatment and conservation.