Occurrence of dry season suppress rubber plantation productivity. Unfortunately, occurrence of drought and deficit rainfall in some regions including Indonesia is predicted to be more frequent in the future. Therefore, researches to select and to identify QTLs for drought resistant rubber clone are needed to be conducted. This research had three steps: determining the best time for chlorophyll-a fluorescence observation, selecting drought tolerant candidate clones using the DFI variable, and detecting QTLs for the DFI (drought factor index) variable. The first topic was carried out to determine the best period for measuring chlorophyll-a fluorescence, which would be used in second research topic. Furthermore, based on the DFI variable, the second research topic was done to identify drought resistant candidate clones from the PB 260 X SP 217 population and to provide genotyping (DFI) data for QTLs analysis. Moreover, the goal of the third research topic was to find QTLs for the DFI variable. The first research found that a dark adaption time of two hours after sunset was sufficient for measuring chlorophyll-a fluorescence transients in rubber leaves without the use of leaf clips. Furthermore, the top ten drought tolerant clones were 34, 206, 056, 007, 205, 225, 066, 235, 109, and RRIM 600, according to the second research. In addition, based on Kruskal-Wallis analysis, the most significant detection of QTL for DFI parameter was found in locus g5TA2155, which is located at 0.553 cM in LG5.