Containing over 5,000 species, Tephritidae is a diverse fly family notorious for containing some of the world’s most destructive fruit pests, including the Mediterranean fruit fly, Oriental fruit fly, South American fruit fly, and Queensland fruit fly. As for most insects, traditional taxonomy has relied primarily on morphological characters to discriminate, define, and describe new species. This has failed to fully resolve some of the most important pest groups, especially those belonging to species complexes, leading to significant debates among the tephritid community. We argue that an integrative approach, correlating independent datasets to the same individual voucher specimens, represents the future of tephritid systematics, taxonomy, and diagnostics. This is particularly important for problematic groups of high biosecurity concern at higher risk of diagnostic confusion.