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Avocados may suffer from short-term waterlogging stress when exposed to high temperatures and heavy rainfall during the summer in Taiwan. We compared the waterlogging responses of own-rooted and grafted seedlings of two Taiwan cultivars, ‘Black-Beauty’ and ‘Hung-Hsin-Yuan’, by stomatal conductance (gs) and chlorophyll fluorescence parameters. Four-day waterlogging and four-day post-waterlogging recovery periods were investigated. Both gs and Fv/Fm of own-rooted seedlings of two cultivars were significant reductions in response to short-term waterlogging. The grafted seedlings on the same cultivar rootstock were evaluated by gs and Fv/Fm during the growth and the growth cessation periods, respectively. The combined responses of gs and Fv/Fm under short-term waterlogging showed that ‘Black-Beauty’ was sensitive to stress because of decreased gs after waterlogging or decreased Fv/Fm after the two-day recovery period. ‘Hung-Hsin-Yuan’ showed more tolerance to waterlogging stress, especially during the growth cessation. This indicates that the vegetative dormancy may affect the evaluation of the stress response of avocados. Our results revealed that gs and Fv/Fm can be effective indicators in the four-day waterlogging of avocado, and the growth status of avocado seedlings should be considered during stress-tolerant variety selection.