The description of the movements and habitat preference of marine fishes is essential to understand their biology and in the evaluation of commercially exploited species and the conservation of endangered ones. In this regard, little is known about the movements of the totoaba (Totoaba macdonaldi), despite its being listed as critically endangered and having been a relevant fishery resource in the past century in Mexico. Totoaba is a fish species endemic to the Gulf of California characterized by late maturation, prolonged life and annual reproduction. Totoaba has maintained its known historical distribution range, although its movements and habitat occupancy in the water column have remained poorly understood. The present study describes, for the first time and at a daily fine scale, the vertical movements and habitat preferences of the totoaba in the Upper Gulf of California. Pop-up satellite archival tags (PSATs) were used to record depth and temperature at 4-minute intervals. Ten individuals were caught and tagged in May 2016 in the Upper Gulf of California and Colorado River Delta Biosphere Reserve. All PSATs were either prematurely released or lost. Data derived from two recovered tags that saved data for 43 and 75 tracking days, respectively, were analysed. The results showed that tagged fishes moved southward to the vicinity of Angel de la Guarda Island; these are consistent with spatial displacement patterns reported in the literature, with a linear displacement of 223 km from deployment to pop-up sites. Fish spent 47% of the time within a depth range of 25–35 m. Depth increased to 70 m for one fish in early summer (late June). The preferred temperature of fishes ranged between 21–23°C. A generalized linear model revealed that vertical movement was influenced by temperature. The vertical displacement of the totoaba shows a diurnal variation that may be associated with the distribution of its prey. Further work is needed to test this hypothesis with a larger number of organisms.