Strawberry is one of the major economic crops in the modern agriculture industry worldwide. Fusarium wilt disease, caused by the Fusarium oxysporum f. sp. fragariae (FOF), is known as the most problematic factor in strawberry production. In a previous study, Streptomyces griseus S4-7 was isolated from the strawberry rhizosphere, exhibited an exceptional antifungal activity against the Fusarium wilt pathogen. However, sensitivity variation to S4-7 in the pathogen population was not evaluated. Therefore, we collected the pathogen nationwide and screened the sensitivity of FOF to the biological agent. A total of 96 FOF isolates was tested their sensitivity to the S4-7 and less-sensitive FOF isolates had lower cell wall degradation than the standard FOF strain. However, gene expression level of the cell wall organization (pkc1, gcn5) was not different between the less sensitive and the standard FOF strains. The results suggested that among the FOF population, some isolates may develop tolerance against a biocontrol agent through complex tolerance mechanisms.