Fucoidan, a sulfated polysaccharide found abundantly in brown algae such as mozuku seaweeds, is classified as a water-soluble dietary fiber. Fucoidan reportedly exerts antitumor, anti-inflammatory, immunomodulatory, antioxidant, whitening, antibacterial, and antiviral activities. Owing to these properties, fucoidan has been widely used as an active ingredient for skin care purposes, including quasi-drug serums and hair growth products. However, fucoidan effects differ depending on the algal species, molecular weight, and other factors. Thus, it is crucial to thoroughly test fucoidan preparations and determine their suitability for individual applications. In this study, we probed the effects of mozuku-derived ultra-high-molecular-weight fucoidan (1700 kDa, normally ~300 kDa) preparations on indigenous skin bacteria and general bacteria. We observed that fucoidan preparations derived from Tongan mozuku Cladosiphon novae-caledoniae and Amami mozuku Cladosiphon okamuranus inhibited the growth of skin bacteria, such as Staphylococcus aureus and Staphylococcus epidermidis. However, no growth inhibition was observed for the skin bacterium Cutibacterium acnes or general bacteria, such as Lactobacillus casei, Escherichia coli, and Bacillus subtilis. Given its ability to hinder the growth of skin disease-causing bacteria, mozuku-derived ultra-high-molecular-weight fucoidan holds promise for future applications in the pharmaceutical and cosmetic industries.