The relationships among the genera of the early-diverging eudicot family Berberidaceae have long been controversial. To resolve these relationships and to better understand plastome evolution within the family, we sequenced the complete plastome sequences of ten Berberidaceae genera, combined these with six existing plastomes for the family, and conducted a series of phylogenomic analyses on the resulting data set. Five of the newly sequenced plastomes were found to possess the typical angiosperm plastome complement of 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. The infA gene was found to be pseudogenized in Bongardia, Diphylleia, Dysosma and Vancouveria; rps7 was found to be severely truncated in Diphylleia, Dysosma and Podophyllum; clpP was found to be highly divergent in Vancouveria; and a similar to 19 kb inversion was detected in Bongardia. Maximum likelihood phylogenetic analyses of a 79-gene, 24-taxon data set including nearly all genera of Berberidaceae recovered four chromosome groups (x = 6, 7, 8, 10), resolved the x = 8 group as the sister to the x = 10 group, and supported the monophyly of the Glade comprising x = 7, 8, 10. The generic relationships within each group were all resolved with high support. Based on gene presence within the Inverted Repeat (IR), a total of seven plastome IR types were identified within Berberidaceae. Biogeographical analysis indicated the origin and diversification of Berberidaceae has likely been strongly influenced by the distribution of its favored habitat: temperate forests.