This data publication contains tabular data with repeat measurements of tree and shrub data for a set of transects located in Stanislaus National Forest (STF) and Yosemite National Park (YOSE) in California. These transects represent part of a systematic timber inventory collected across a large mixed-conifer dominated landscape by the U.S. Forest Service in 1911. Trees were tallied by species, diameter and height within 40 x 400 meter (m) strips that spanned the center of quarter-quarter sections (QQs) delineated by the Public Land Survey System. Shrub cover was determined using an ocular estimate. Repeat data were collected in either 2005, 2007 or 2013 in three to four 0.1 hectare circular plots (radius 17.8 m) per transect, centered at random, non-overlapping distances along the historical transect centerline. This data publication therefore contains measurements such as the percentage cover of shrubs for multiple species, basal area of dead and live conifer trees, and density of live conifer trees with various diameters at breast height for both STF and YOSE in 1911 and the remeasurement year of 2005, 2007, or 2013.