The increasing use of chemical control agents and pesticides to prevent plant disease has resulted in several human and environmental health problems. Seaweeds, e.g., Amphiroa anceps extracts, have significant antimicrobial activities against different human pathogens. However, their anti-phytopathogenic activities are still being investigated. In the present investigation, three fungal isolates were isolated from root rot and grey mold symptomatic strawberry plants and were molecularly identified by ITS primers to Fusarium culmorum, Rhizoctonia solani, and Botrytis cinerea with accession numbers MN398396, MN398398, and MN398400, respectively. In addition, the organic extract of the red alga Amphiroa anceps was assessed for its antifungal activity against the three identified fungal isolates and tobacco mosaic virus (TMV) infection. At 100 µg/mL, the A. anceps extract had the best biological activity against R. solani, B. cinerea, and TMV infection, with inhibition rates of 66.67%, 40.61%, and 81.5%, respectively. Contrarily, the A. anceps extract exhibited lower activity against F. culmorum, causing inhibition in the fungal mycelia by only 4.4% at the same concentration. The extract’s HPLC analysis revealed the presence of numerous phenolic compounds, including ellagic acid and gallic acid, which had the highest concentrations of 19.05 and 18.36 µg/mL, respectively. In this line, the phytochemical analysis also showed the presence of flavonoids, with the highest concentration recorded for catechin at 12.45 µg/mL. The obtained results revealed for the first time the effect of the A. anceps extract against the plant fungal and viral pathogens, making the seaweed extract a promising source for natural antimicrobial agents.