The in vitro effects of UVBR were investigated in apical segments of Hypnea musciformis. The plants were cultivated and exposed to photosynthetically active radiation (PAR) at 80 μmol photons m−2 s−1 and PAR + UVBR at 1.6 W m−2 at 3 h per day for 7 days. Toluidine Blue reaction showed metachromatic granulations in vacuole, and Periodic Acid Schiff stain showed a decrease in the number of floridean starch grains. UVBR also caused changes in the ultrastructure of cortical cells, which included increased thickness of the cell wall, reduced intracellular spaces, changes in the cell contour, destruction of chloroplast internal organization, and rough endoplasmic reticula increase. The algae cultivated under PAR-only showed growth rates of 9.7% day−1, while algae exposed to PAR + UVBR grew only 3.2% day−1. Furthermore, compared with control algae, phycobiliprotein contents (phycoerythrin, phycocyanin, and allophycocyanin) were observed to decrease after PAR + UVBR. However, chlorophyll a levels were not significantly different (ANOVA, P = 0.52) after exposure to PAR + UVBR. As a photoprotective adaptation strategy against UVB damage, an increase of 58.9% phenolic compounds and 3.6% of carotenoids was observed. Overall, these results lead to the conclusion that both ultrastructural damage and observable changes in metabolism occurred in H. musciformis after only 3 h of daily UVB exposure over a 7-d experimental period.