The fruit fly, Drosophila melanogaster, patterns its segments rapidly and simultaneously, via a mechanism that relies on the ability of transcription factors to diffuse between blastoderm nuclei. Ancestral arthropods patterned posterior segments sequentially in a cellular environment, where free diffusion was likely to have been inhibited by the presence of cell membranes. Understanding how the Drosophila paradigm evolved is a problem that has interested evolutionary developmental biologists for some time. In this article, I review what is known about arthropod segmentation (...) mechanisms, and present a model for the evolution of the Drosophila paradigm. The model predicts that the primary pair‐rule genes of Drosophila ancestrally functioned within and/or downstream of a Notch‐dependent segmentation clock, their striped expression gradually coming under the control of gap genes as the number of segments patterned simultaneously in the anterior increased and the number patterned sequentially via a segmentation clock mechanism in the posterior correspondingly decreased. BioEssays 26:1108–1116, 2004. © 2004 Wiley Periodicals, Inc. (shrink)