Carijoa riisei is an invasive octocoral whose dispersal in the tropics has increased considerably in recent years. This study evaluated the changes in the benthic fauna assemblages associated with C. riisei growing on rocks from a sea port and on the metal of a submerged shipwreck in the bays of Manzanillo, Colima, in the Mexican Central Pacific. Quarterly samples were collected between April 2021 and January 2022, with the presence or absence of C. riisei. The effect of C. riisei on the benthic fauna according to the type of substrate was evaluated with PERMANOVA models. The presence of C. riisei was found to affect taxonomic diversity. In the absence of the octocoral, 209 species were recorded, whereas in its presence, 190 were found. The decline of taxa occurred at the level of families, genera, and species. The interaction of the presence/absence of C. riisei and substrate generated significant changes in the Shannon (1D) and Simpson (2D) diversity indexes. However, the presence of C. riisei coincided with higher abundances of Ophiothela mirabilis, Ericthonius brasiliensis, and Pseudobranchiomma schizogenica. In conclusion, the snowflake coral favors the dominance of some species and reduces the biological diversity of several taxa, mainly mollusks, polychaetes, sipunculids, and anthozoans, generating significant changes in the structure of benthic communities. This study highlights the need to evaluate species composition in areas where the octocoral grows, to determine whether its presence has an ecological impact and whether control measures are required.