The Alpine lifezone of California is a unique environment with a distinct biota, including a number of rare endemic species. During the Pliocene and Pleistocene epochs, shifts in global climate caused the growth and recession of alpine glaciers. These glacial events affected organisms that now inhabit alpine ecosystems, causing distributional range shifts, changes in population size, and alternating periods of isolation and population admixture. While the history of glaciation is well understood in California, it is not clear how alpine species responded to glacial events. Understanding the history of these species provides an opportunity to examine how rapid and repeated environmental change influences evolutionary diversification and population dynamics. Several hypotheses are proposed to account for the geographical origin and contemporary pattern of genetic variation in Sierra Nevada alpine species. Population genetic evidence is examined in a diverse set of alpine insects in order to infer the demographic response to climate change and the geographic pattern of diversification. Chapter 1 focuses on alpine butterflies in the Parnassius phoebus complex, which are broadly distributed in western North American mountain ranges. Genetic results indicate a strong population expansion event during the present interglacial phase, as well gene flow from the Rocky Mountains into California during the last glacial phase. Chapter 2 examines the butterfly Colias behrii and finds similar evidence of population expansion during the present interglacial phase and recent connectivity to the Rocky Mountains. Notably, phylogenetic relationships of this butterfly are complicated by alternate genealogical signals from mitochondrial and nuclear DNA, which might be explained by rare hybridization and the transmission of Wolbachia parasites. Chapter 3 focuses on low vagility insects in the genus Grylloblatta , which show a deep lineage break in the northern and southern Sierra Nevada. Genetic diversification within alpine Grylloblatta is synchronous across multiple populations and temporally coincident with periods of glacial advance. Chapter 4 focuses on three species of endemic ground beetles, Nebria ovipennis, N. spatulata, and N. ingens, which exhibit increasingly restricted altitudinal zonation, respectively. These species have different patterns of population substructure, with N. ingens showing evidence of north-south lineage diversification in the Sierra Nevada.