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Populations of the Mojave Desert Tortoise (Gopherus agassizii) experienced severe declines in abundance in the decades leading up to 1990, when the species was listed as threatened under the U.S. Endangered Species Act. Population responses to recovery efforts have not been well documented because of the difficulties of studying this low-density, cryptic species over a time period appropriate to its long generation time. We used line distance sampling to estimate annual adult densities since 1999 in Utah and since 2004 elsewhere in the range of Mojave Desert Tortoises. We used generalized least squares regression on log-transformed adult tortoise densities to estimate annual percentage change through 2014 in each of 17 Tortoise Conservation Areas (TCAs) in the five recovery units. We report annual proportional increases in density of adults in the Northeastern Mojave Recovery Unit, but declines in the other four recovery units. Adjusting these densities and trends for the area of potential habitat in each recovery unit, we estimated that in 2004 there were 336,393 adult tortoises (standard error [SE] = 51,596), with an overall loss of 124,050 adult tortoises (SE = 36,062) by 2014. The proportion of juveniles in our surveys has been decreasing in all five recovery units since 2007. Prevailing declines in the abundance of adults overall and in four of the five recovery units indicate the need for more aggressive implementation of recovery actions and more critical evaluation of the suite of future activities and projects in tortoise habitat that may exacerbate ongoing population declines.