Acne is one of the most common dermatological conditions, peaking during adolescence and early adulthood, affecting about 85% of individuals aged 12–24. Although often associated with teenage years, acne can occur at any age, impacting over 25% of women and 12% of men in their forties. Treatment strategies vary depending on the severity, including the use of topical gels or creams containing benzoyl peroxide and retinoids, antibiotics, and systemic or topical isotretinoin. However, these treatments can cause irritation, allergies, and other toxic side effects. Currently, there is no natural-based alternative for antibacterial photodynamic therapy targeting acne using marine drugs or extracts. Through a bioguided screening approach, we identified the ethanol extract of Skeletonema marinoi as highly phototoxic against three bacterial species associated with acne—Cutibacterium acnes, Staphylococcus aureus, and Staphylococcus epidermidis. This extract exhibited phototoxicity in planktonic bacteria under white and red light, disrupted bacterial biofilms, reduced sebum production but also showed phototoxicity in keratinocytes, highlighting the importance of the specific targeting of treatment areas. Further investigations, including fractionation and high-resolution structural analysis, linked the observed phototoxicity to a high concentration of pheophorbide a in the extract. Given its notable in vitro efficacy, this extract holds promising potential for clinical evaluation to manage mild acne. This discovery paves the way for further exploration of Skeletonema pigment extracts, extending their potential applications beyond acne phototherapy to include dermocosmetics, veterinary medicine, and other phototherapy uses.