Losses in the production of avocado (Persea americana (Mill.)) are incurred due to Phytophthora root rot (PRR), a disease of the feeder roots that results in tree-dieback and eventual tree death. Avocado is also a flood-sensitive species and flooding exacerbates the effects of PRR. The avocado industry relies on the use of rootstocks tolerant to PRR to minimise losses. The present study compared the gas exchange and chlorophyll fluorescence responses of avocado rootstock plants of ‘Dusa™’, the current South African industry standard, with ‘Duke 7’, and the selections R0.12 and R0.06 which show reduced and superior tolerance to PRR, respectively. A decline in stomatal conductance (g s ) and net CO 2 assimilation (P N ) over the 30day evaluation period were early responses to flooding. ‘Dusa™’, the more tolerant rootstock plants, demonstrated a better recovery in P N and g s in response to inoculation; however, both rootstocks performed poorly under flooded conditions. A decline in P N in infected ‘Duke 7’ plants appeared to be associated with stomatal limitations due to reduced stomatal conductance. The decline in P N and g s was not apparent in infected ‘Dusa™’ plants. Non-stomatal limitations to P N in rootstock plants exposed to flooding were also evident as indicated by increases in the ratio of internal to atmospheric CO 2 concentrations (C i /C a ). Impaired photosynthetic capacity in flooded rootstock plants was reflected by reduced photosystem II efficiency and photochemical quenching. In comparison to ‘Dusa™’, R0.12 rootstock plants showed reduced P N and g s following inoculation with Phytophthora cinnamomi whereas the more tolerant R0.06 rootstock plants revealed sustained photosynthetic activity. Interestingly R0.06 was the only rootstock able to maintain P N and g s in non-inoculated, flooded plants.