Species experience very different selective pressures across their latitudinal range yet the genetic changes that underlie fitness differences across latitudes are unknown. Salmon show extreme degrees of local adaptation to environments. Here, we sequence 137 whole-genomes of chinook salmon (Oncorhynchus tshawytscha) across the North American pacific coast to study how local adaptation to latitude has evolved. We focus first on five known candidate genes related to timing of migration and maturation, and then discover additional targets of selection showing strong latitudinal clines. Allelic variation in all five candidate genes was steeply associated with latitude. These five genes play connected roles in major genetic pathways underlying growth, maturation, and timing of life histories, such as the MAPkinase, the clock genes, the Wnt and the hippo pathways active in the eye, the suprachiasmatic nucleus, the hypothalamus, the pituitary gland and gonads. We discovered surprisingly strong correlations with latitude in many other genes of these same pathways. Such a large-scale coordinated transformation of so many genes that interact to determine key life history variables goes some way toward explaining the strength of local adaptation from north to south, with implications for the conservation of this iconic species and its adaptation to future climates.