The degree of tolerance to adverse conditions ultimately shapes a species' vulnerability to environmental changes. Some studies have reported limited thermal tolerance due to hypoxia in fish employing aquatic respiration. However, there is a lack of information regarding the effects of hypoxia on thermal tolerance in fish exhibiting bimodal respiration. A set of Amazonian fish species has adaptations to breathe air when oxygen in water is not enough to fulfil demand. Additionally, loricariid species within this group possess stomach adaptations for air breathing. The Loricariidae family exhibits varying stomach types and observed morphological differences could influence their ability to obtain oxygen from the air. This ability may, in turn, have consequences for the thermal tolerance of these species. Our objective was to assess the effects of hypoxia on thermal tolerance, along with the physiological (whole-animal metabolic rates and mitochondrial respiration) and behavioural mechanisms involved, in two facultative air-breathing species: Pterygoplichthys pardalis and Ancistrus dolichopterus. These species showcase morphological distinctions in their stomachs, with the former having a higher capacity to obtain oxygen from the air. Thermal tolerance in P. pardalis remained unaffected by dissolved oxygen in the water when air access was available but decreased when access to the water surface was restricted, specifically in hypoxic conditions. Conversely, the thermal tolerance of A. dolichopterus decreased below the critical oxygen partial pressure (Pcrit), even with access to air, highlighting their limited ability to obtain oxygen through their adapted stomach. Our results underscore that air breathing enhances thermal tolerance, but this effect is prominent only in species with a higher capacity for air breathing.