AbstractClimate‐modulated parasitism is driven by a range of factors, yet the spatial and temporal variability of this relationship has received scant attention in wild vertebrate hosts. Moreover, most prior studies overlooked the intraspecific differences across host morphotypes, which impedes a full understanding of the climate–parasitism relationship. In the common lizard (Zootoca vivipara), females exhibit three colour morphs: yellow (Y‐females), orange (O‐females) and mixed (mixture of yellow and orange, M‐females). Zootoca vivipara is also infested with an ectoparasite (Ophionyssus mites). We therefore used this model system to examine the intraspecific response of hosts to parasitism under climate change. We found infestation probability to differ across colour morphs at both spatial (10 sites) and temporal (20 years) scales: M‐females had lower parasite infestations than Y‐ and O‐females at lower temperatures, but became more susceptible to parasites as temperature increased. The advantage of M‐females at low temperatures was counterbalanced by their higher mortality rates thereafter, which suggests a morph‐dependent trade‐off between resistance to parasites and host survival. Furthermore, significant interactions between colour morphs and temperature indicate that the relationship between parasite infestations and climate warming was contingent on host morphotypes. Parasite infestations increased with temperature for most morphs, but displayed morph‐specific rates. Finally, infested M‐females had higher reductions in survival rates than infested Y‐ or O‐females, which implies a potential loss of intraspecific diversity within populations as parasitism and temperatures rise. Overall, we found parasitism increases with warming temperatures, but this relationship is modulated by host morphotypes and an interaction with temperature. We suggest that epidemiological models incorporate intraspecific diversity within species for better understanding the dynamics of wildlife diseases under climate warming.