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The mechanisms and symptoms of graft incompatibility were investigated using Sturt's Desert Pea (SDP, Swainsona formosa) grafted onto SDP, Parrot's Bill (PB, Clianthus puniceus), Senna artemisioides and Acacia terminalis. From the results of previous experiments, SDP/PB and SDP/SDP were regarded as graft compatible combinations, and SDP/Senna and SDP/Acacia were regarded as graft incompatible combinations. Four weeks after grafting, continuing vascular tissues from rootstocks to scions were observed at the graft unions of compatible combinations. With incompatible combinations, parenchyma cells (calli) were observed between vascular bundles of rootstocks and those of scions, and no vascular connections were observed at the graft unions. At 4 weeks after grafting, increased fresh weight, dry weight, weight ratio and concentrations of inorganic mineral nutrients were obtained in scions of compatible combinations, compared to those of incompatible combinations. The breaking weight of the graft union of compatible combinations was bigger than that of incompatible combinations. Increased peroxidase activities were obtained in SDP scions grafted onto incompatible rootstocks. It was discovered that higher CO2 concentrations occurred around grafted plants of compatible combinations than those of incompatible combinations.