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Geographic variation in 23 to 29 protein‐encoding genetic loci was examined in 48 populations of the Ensatina complex, a “ring species” distributed around the Central Valley of California. The samples span two critical links in the chain of morphologically distinct units: the transition from the unblotched to blotched color pattern types in the vicinity of Lassen Peak, northeastern California, and a geographic gap in the range of the complex in the San Gabriel Mountains, southern California. A general pattern of isolation by distance with a regular buildup of genetic distance correlated with increases in geographic distance characterizes the populations studied, with the exception of a little‐differentiated group of populations in the northern Sierra Nevada; this region is postulated to be a zone of genetic reticulation characterized by relatively high gene flow. An adaptively significant color pattern is thought to have …