Abstract: Appropriate reference genes for specific experimental materials and conditions are critical for analyzing the expression of target gene by real-time quantitative PCR. In this study, four common housekeeping genes GAPDH, Actin, UBQ, CYP and two novel reference genes CACS, F-box were chosen for identifying the expression stability in Benincasa hispida Cogn. var. chieh-qua How samples from various plant tissues (roots, stems and leaves) or under fusaric acid (FA) stress. The expression stability of candidate genes was determined and ranked using RefFinder software. The results revealed a remarkably stable expression pattern of Actin and F-box when samples were stressed by fusaric acid. F-box gene showed the most stable expression level in different tissues. Additionally, expression of traditional housekeeping genes GAPDH and CYP showed great variations and therefore they were considered unsuitable as reference genes. This study has laid the foundation for the study of resistance-related genes expression for fusarium wilt in B. hispida Cogn. var. chieh-qua How