Yosemite is one of the largest and least fragmented habitat blocks in the Sierra Nevada, and the park supports a diversity of plants and animals. The park has an elevation range from 2,000 to 13,114 feet and contains five major vegetation zones: chaparral/oak woodland, lower montane, upper montane, subalpine, and alpine. Of California's 7,000 plant species, about 50% occur in the Sierra Nevada and more than 20% within Yosemite. There is suitable habitat or documentation for more than 160 rare plants in the park, with rare local geologic formations and unique soils characterizing the restricted ranges many of these plants occupy.

The geology of the Yosemite area is characterized by granite rocks and remnants of older rock. About 10 million years ago, the Sierra Nevada was uplifted and then tilted to form its relatively gentle western slopes and the more dramatic eastern slopes. The uplift increased the steepness of stream and river beds, resulting in formation of deep, narrow canyons. About 1 million years ago, snow and ice accumulated, forming glaciers at the higher alpine meadows that moved down the river valleys. Ice thickness in Yosemite Valley may have reached 4,000 feet during the early glacial episode. The downslope movement of the ice masses cut and sculpted the U-shaped valley that attracts so many visitors to its scenic vistas today.