Under changing climate, plants need combined ability to cope with co-occurring biotic/abiotic stresses. Understanding simultaneous plant responses to multiple stresses offers unique insights towards developing effective strategies to mitigate effects of such stresses in plants. Quantitative reverse transcription PCR was used to determine and compare relative gene expression ratios (RGERs) of three disease resistance-related genes, chalcone synthase, GA protein, and phenylalanine ammonia lyase (PAL), and three abiotic stress-related genes, a LRR receptor-like protein kinase (RPK), heat shock protein 81, and Trifolium repens cold responsive protein, across seven durations of infection by the root pathogen Pythium irregulare under three temperature regimes in three Trifolium subterraneum varieties of varying resistance. Temperature and genotype drove biotic and abiotic stress-related gene expression in Pythium-infected plants. RGERs of tested genes and their relationships differed across varieties, temperatures, and infection duration (ID). These are the first studies to report expression of defence-related genes in relation to either biotic or abiotic stress in subterranean clover. The current study not only demonstrates how RGERs of tested genes and their relationships differ across varieties, temperatures, and ID, but also highlights as yet unexploited opportunities to use these biotic/abiotic-related genes together to develop new varieties with combined biotic/abiotic stress resistances in forage legumes that are suitable for changing climate scenarios. Examples could include RGERs of PAL to identify “temperature-stable” disease-resistant varieties, and RGERs of RPK to eliminate susceptible and temperature-sensitive genotypes.