The widely distributed genus Codium is a major component of the marine macroalgal flora and has its largest species diversity in warm-temperate regions. Along the South coast of Australia, Codium is a diverse group, but the species diversity in the easternmost region of Victoria is not well-documented. In this study, we characterized the species diversity of Codium from Croajingolong National Park, Gabo Island Lighthouse Reserve and Cape Howe Marine National Park. The specimens were collected from a wide range of microhabitats during an expedition of the Bush Blitz program, and Codium species were delimited through a combination of molecular analyses of the chloroplast markers tufA and rbcL, and morphological observations. Six species-level clusters were found, corresponding to the native C. australicum, C. harveyi, C. lucasii.1 and C. fragile subsp. novae-zelandiae; and the exotic C. fragile subsp. fragile and C. tenue. The specimens of C. australicum showed variability in the architecture of the thallus that was attributed to the different habitats where they were collected. The utricles of C. harveyi were unusual in having a thick apical cell wall that protruded inwards and had internal projections. The species found in eastern Victoria are typical of the Flindersian and Peronian biogeographic provinces, and the low diversity of Codium species in this region is comparable to that of New South Wales.