Codium fragile ssp. tomentosoides is one of the five most invasive macroalgae worldwide. We compared epiphytic assemblages between native (ssp. tasmanicum and ssp. novae-zelandiae combined) and non-indigenous (ssp. tomentosoides) subspecies of Codium fragile on three rocky intertidal shores in southeast Australia. Twelve species of epiphytes covered up to 20% of the surface of both native and non-indigenous Codium subspecies, but none were unique to either subspecies. For C. fragile subspecies, epiphytic cover declined from the lower (older) parts of the thallus to the branch tips. The abundance and species composition of epiphytes differed significantly between native and non-indigenous C. fragile, but differences varied among rocky shores. Results demonstrate that non-indigenous C. fragile does not play a functionally similar role to closely related native Codium subspecies. Spatial differences in epiphytic assemblages between Codium subspecies among rocky shores demonstrate that effects of non-indigenous species may be strongly location specific. Thus, our study emphasises the need to investigate variation in the effects of invaders across the regional landscape.