Cultivated apple (Malus × domestica Borkh.), one of the most widely produced and agronomically important fruit crops in temperate regions, has been domesticated from M. sieversii in the Tian Shan Mountains since 4,000-10,000 years ago and dispersed from Central Asia to West Europe along the Silk Route, allowing hybridization and introgression from wild crabapples. Apple domestication is mainly related to two wild species: M. sieversii as the primary progenitor and M. sylvestris as a major secondary contributor. Centuries of human exploitation and selection have produced several thousand apple cultivars with diverse fruit sizes and flavors, the majority of which are maintained in germplasm repositories, leaving only a few dozen elite cultivars grown worldwide for fruit production. Unlike seed-propagated annual crops with intensive artificial selections and selfing peach with recent domestication bottlenecks, apple has a slow, weak, and complex domestication process with intensive wild-introgressions because of their lengthy juvenile phases, self-incompatibility and wide usage of vegetative propagation. Little information is available about genomic responses to the artificial selections in apple. In this study, we performed deep genome sequencing of 97 diverse apple accessions. The large amount of genomic variation resources has allowed us to gain new insights into apple evolution and domestication processes, which may help accelerate the usage of wild species in apple breeding practice.