Strawberry anthracnose, caused by Colletotrichum nymphaeae is an important disease of strawberry. In this study, an endophytic bacterium isolated from the stem of Fragaria × ananassa cv Paros and identified as Serratia rubidaea strain Mar61-01 based on phenotypic, biochemical characteristics and molecular phylogenetic analysis. Antagonistic activities of this endophytic bacterium against C. nymphaeae were investigated under in vitro, in vivo and greenhouse conditions. The strain Mar61-01 reduced mycelial growth and conidial germination of C. nymphaeae in in vitro tests. Furthermore, it reduced disease severity on inoculated strawberry fruits and seedlings compared with uninoculated control. In addition, the strain Mar61-01 produced prodigiosin pigment. The pigment was purified by thin layer chromatography and its chemical structure was characterized by FT-IR and NMR (400 MHz) spectra. The results indicated that prodigiosin is a key feature in biocontrol of C. nymphaeae. The inhibition growth of C. nymphaeae under in vitro, in vivo, and greenhouse conditions showed that S. rubidaea Mar61-01 has the potential for managing of strawberry anthracnose.