Cell fates in the anterior and posterior termini of the Drosophila embryo are programmed by multiple zygotic genes that are regulated in response to a maternally encoded signal transduction pathway. These genes specify terminal as distinct from central cell fates, program pattern along the anteroposterior and dorsoventral axes of the termini, and also control endoderm specification and terminal morphogenetic movements. Here, we use a genetic interaction test to dissect the zygotic components of the terminal genetic hierarchy. We show that two genes, lines and empty spiracles, act downstream of tailless to repress central and promote terminal cell fates along the anteroposterior axis of the termini. Genes that control dorsoventral pattern in the termini and genes that program terminal morphogenesis act in distinct branches of the genetic hierarchy that are independent of tailless.