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In order to screen out the most stable reference genes in tomatoes under powdery mildew (PM) stress and study the expression of related genes in the interaction between tomato and PM more accurately, this study will provide a calibration basis for the expression of related functional genes. In this study, the expression stabilities of eight tomato candidate reference genes of <i>EF1α</i>, <i>L33</i>, <i>Act</i>, <i>Ubi</i>, <i>GAPDH</i>, <i>UK</i>, <i>CAC</i> and <i>TIP41</i> in susceptible tomato and resistant tomatoes under PM stress were ranked using four different computation programs, including geNorm, Normfinder, BestKeeper and the comparative ∆CT method. Then RefFinder was used to analyze the ranking results of four kinds of software comprehensively. Finally, the selected reference genes were validated by the target gene <i>SlMLO1</i>. The results of geNorm showed that the normalization of qRT-PCR using two reference genes could meet the requirements. The comprehensive analysis of RefFinder showed that the most stable reference genes were <i>Act</i> and <i>EF1α</i> for both tomato varieties. The combination of <i>Act</i> and <i>GAPDH</i> was most stable in susceptible tomato ‘MM’. The combination of <i>Act</i> and <i>EF1α</i> was most stable in resistant tomato ‘62579′. Generally, the <i>Act</i> was the most stable reference gene in the two tomato varieties under PM stress. This study will lay a foundation for the related functional gene expression research in tomatoes under PM stress.