Changes in chlorophyll florescence is one of the physiological responses of plants to waterlogging stress. Due to easily measured in field and its inexpensive and non-destructive characteristics, it is one of the best ways to assess different genotypes tolerance to stresses. In this experiment, trends of chlorophyll fluorescence index (Fv/Fm) of ‘Satsuma’ mandarin (Citrus unshiu) on seven rootstocks (sour orange, Swingle citromello, Carizo citrange, Troyer citrange, C-35, Smooth flat sevil and Gou tou) were determined in some soils of East Mazandaran. The experiment was conducted as factorial in a randomized complete block design. The results showed that effect of different factors on changes of chlorophyll fluorescence were significant. Soils 7 and 1 had the highest and lowest index, respectively. The effect of different rootstocks on fluorescence index showed that with increasing duration of waterlogging, this index drops increasingly compared to the beginning of waterlogging. Gou tou and Sour orange had the highest and lowest fluorescence during waterlogging, and Swingle, Carizo, Troyer, Smooth and C-35 placed after Gou tou, respectively. In addition, tolerance of rootstocks to waterlogging was different in various soils of this area.