At first look, the harsh physical conditions of the Andes should impose serious physiological constraints on hummingbirds, but instead, they have a wide distribution and are abundant at high altitudes. Several studies suggest highland species are well adapted to these harsh conditions. Genetic adaptation is difficult to study in non-model organisms, especially as laboratory experiments are impractical for long-lived species. However, new genomic methods have revealed specific amino acid changes, genes, and biochemical pathways that are repeatedly involved in adaptation to survival in high altitude environments. My dissertation research addresses two questions: 1) What is the genetic basis for high-altitude adaptation in Andean hummingbirds? And 2) Are the mechanisms the same across divergent taxa and populations? I generated transcriptome data for 12 Andean hummingbird species occurring from low to high elevations that independently colonized the Peruvian Andes. Parallel molecular evolution can occur at any of several hierarchical levels of biological organization. I identified parallel evolution across highland species for several pathways, including those related to cellular respiration and cell death, but the genes and mutations often differed. I next examined these questions for populations of lowland and highland species in the Peruvian Andes. I conducted an exon capture sequencing experiment to map their spatial population genomic variation and to test for associations between genetic patterns and elevation while accounting for demographic history. I found that isolation by distance and physical barriers play principal roles in shaping spatial population genomic variation. In addition to population divergence, I also identified clinal variation in allele frequencies across elevation for SNPs in several genes with previous links to highland adaptation. Collectively, my results for Andean hummingbird species and populations indicate there is predictability in the genetic mechanisms of adaptation to high altitude, though there are a variety of adaptive paths. By investigating how organisms evolved to thrive in challenging environmental conditions, we can illuminate the mechanisms of evolution and refine future study of the units on which evolution acts.