Climate change and biological invasions are two of the major threats to biodiversity. They could act synergistically to the detriment of natives as non-native species may be more plastic and resilient when facing changing environments. The twoline skiffia (Skiffia bilineata) is an endangered Mexican topminnow that cohabits with invasive guppies (Poecilia reticulata) in some areas in central Mexico. Guppies have been found to take advantage from associating with the twoline skiffia and are considered partially responsible for the decline of its populations. Refuge use and exploratory behaviours are trade-offs between being safe from the unknown and the opportunity to explore novel areas in search for better resources or to disperse. The aim of this study is to investigate how a change in temperature affects the refuge use and exploratory behaviours for both species. We found that temperature affects the refuge use of twoline skiffias, and the swimming activity of both species. Skiffias explored the rock more than guppies regardless of the temperature scenario. Also, smaller fish spent more time performing exploratory behaviours than bigger ones. Our study is the first to test the effect of temperature on the refuge use and exploratory behaviour of a goodeid species, and our results contribute to the idea that some natives could be more affected by climate change than some invaders.