The nuclear gene period is used to reconstruct the phylogeny of Anastrepha, a genus of tephritid fruit flies. Specifically, a region of period termed C3C5 that is located in the dCLK:CYC inhibition domain (CCID) is analyzed. This is the first study using this C-terminal region of the period gene for phylogenetics. Variation in the gene is informative for this genus, and period trees are compared with phylogenies based on mitochondrial and morphological data sets. In general, branches that are supported in the other data sets are recovered in the period tree; moreover, trees built using the period gene support branching patterns previously unresolved with 16S rRNA gene data. Important relationships recovered in the period gene tree include a paraphyletic placement of Anastrepha with respect to Toxotrypana, support for the separation of Anastrepha species groups into two evolutionary sections (with the exception of the pseudoparallela species group), and evidence that several species groups are not monophyletic.