This species is notable for its well developed, unequal calyx lobes. It is similar to Gaertnera humblotii and G. phyllostachya. Gaertnera raphaelii may hybridize with G. phanerophlebia, in particular one specimen, P.J. Rakotomalaza et al. 2068, appears to represent a hybrid of G. phanerophlebia with either G. humblotii or G. raphaelii.