Water deficit stress is a main constraint on plant growth and crop production. Cassava can cope with soil water deficit condition but the stress can trigger a wide variety of responses including alterations in physiological, biochemical and molecular levels which make plant gene regulatory network system more complicated and difficult to evaluate. ‘Huay Bong 60’ (HB) and ‘Hanatee’ (HN) cultivars were subjected to well-watering and water stress conditions for 3 and 6 days, and rewatering for 3 days. The chlorophyll fluorescence parameters, Fo, Fm and Fv/Fm, were measured. The water deficit stress induced an increase in the Fo in both cultivars accompanied by a decrease in the Fm and the Fv/Fm until 6 days of stress. When rewatering was applied at day 7, all parameters were comparable to the control (day 0) plant but the parameters measured 3 days of rewatering had the opposite direction. However, the Fv/Fm value showed the normal level (~0.8) for all stress period and stress release. This indicates the two cassava cutivars have potential to survive under water deprivation without physiological changes. GeneFishingTM method was performed for identification of transcripts in HB cultivar under stress. Five differentially expressed genes (DEGs) were homologous to hypothetical proteins with unknown function, and 3 DEGs were unidentified sequence. Twenty-three DEGs showed sequence similarity to several known protein functions including the predicted signal transduction protein, metalloprotease, chlorophyll A-B binding protein, thioredoxin, Leucine Rich Repeat and Ca2+ binding protein.