Abstract Many selective pressures modulate microhabitat choice of ectotherms, such as temperature, humidity and habitat heterogeneity, and these vary in space and time. Here we analysed: 1) microhabitat selection comparing characteristics of stones (and their surroundings) under which geckos (Tarentola delalandii, mainly nocturnal) were found during the day with that of stones selected randomly; 2) relationship of a measure of body size to microhabitat characteristics (stone and herb covers, etc., and temperature/humidity) and cloacal temperature of males, females and juveniles from two contrasting habitats of Tenerife (northern and southern localities) and in two periods of the year (Spring-Summer and Autumn-Winter). In comparison with randomly selected stones, geckos significantly selected stones with lower temperature in the Spring-Summer and microhabitats with high stone cover. Gecko size was significantly larger in the Northern than in the Southern locality, in spring – summer than in autumn – winter and in males than in females. In both populations and time periods, the largest body sizes were significantly associated with higher environmental and shelter temperatures and with low values of humidity and stone cover. Cloacal and shelter temperatures were positively and significantly related; at higher values of the latter, juveniles attained significantly higher temperatures than adult males but lower than that of females. Larger body size was associated with high shrub and leaf litter covers and high values of shelter dimensions. Therefore, we suggest that in relation to their body sizes, geckos seem to select their shelters considering specific microhabitat characteristics surrounding them that may provide thermoregulatory and/or antipredator profits.