Climate change is increasing the frequency of temperature changes in aquatic environments potentially affecting host microbiota. Microbiota composition can also be affected by host genotype and therefore it is important to understand effects of a stressor across genetically different populations. Size-selective harvesting is an example of an anthropogenic stressor, that drives genetic change in exploited populations. To examine the effects of water temperature and host genotype on skin microbiota, we used three zebrafish selection lines and exposed them to three temperatures: elevated (34 °C), ambient (28 °C), and low (22 °C) for 250 days. Thermal stress had no significant impact on skin microbiota alpha-diversity but did elicit a small, but significant change in microbiota composition (beta-diversity) that included an increase in relative abundance of pathogenic bacteria (e.g., Vibrio) and altered microbiota network structure. By contrast, selection lines (genotypes) did not significantly differ in skin microbiota alpha- or beta-diversity. Our results suggest that skin microbiota is not profoundly impacted by either thermal stress or genotype but may become more prone to an increase in pathogenic taxa under thermal stress. Our results contribute to the understanding of how the interactions of anthropogenic stressors (thermal stress and size-selective harvesting) may potentially affect fish health and fitness.