Systematics and evolutionary biology are being bolstered by a renaissance in cytogenetics and comparative genomics as illustrated by reviewing Peter Raven's integration of cytogenetics and phylogenetics and by presenting updates to his work in three key research areas. The first area is the evolution of chromosomes during the origin of the angiosperms. Raven's analysis of chromosome numbers in the Annonales and other basal angiosperms inspired modern genomic comparisons that have revealed paleopolyploid events, which appear to have occurred early and often during flowering plant diversification. Second, Raven's characterization of chromosome evolution in various genera of Onagraceae is updated in light of a contemporary Onagraceae phylogeny. The possible construction of ancestral karyotypes in the Onagraceae is feasible using techniques that have been successful in analyses of genomic blocks in the Poaceae and Brassicaceae. Third, Raven's work on catastrophic speciation identified the importance of chromosomal rearrangements in the evolution of Clarkia Pursh and the ability of new species to inhabit different environments. Current work in Brassica L. has shown that phenotypic changes contributing to speciation events can arise from relatively few chromosomal rearrangements. A fusion of systematics and cytogenetics is opening new areas of research, with phylogenomics allowing ancestral genome reconstruction, the incorporation of genome-level characters into phylogenetic analyses, and new theories about evolution on a genomic scale.