We studied the structural habitat use and the thermal ecology of Gonatodes humeralis (Guichenot, 1855) in São Luís, Maranhão, Brazil, to examine intersexual differences in the use of perch features and to simultaneously analyze reciprocal differences on thermal ecology between the sexes. Gonatodes humeralis body temperature was strongly correlated with environmental temperatures (air and substrate), but air temperature had an additional effect on the males' body temperatures after removing the effect of the substrate temperature. Males and females differed significantly in perch height use above ground (males perched higher) but the sexes did not differ in the trunk perimeter used. Gonatodes humeralis tended to use the larger tree trunks available in its environment and selected trunks with deeper leaf litter at the base. It is hypothesized that choosing tree trunks with deeper leaf litter is a defensive behavior against predation.