Vaccinium macrocarpon, the most cultivated species of cranberry, hosts a large spectrum of pathogenic fungi responsible for 25-33% of production losses through cranberry fruit rot (CFR). Given that many fungal species can be involved in CFR, the diagnosis of the disease has always been challenging. To overcome this problem, a new molecular tool was recently developed to diagnose the 12 most important fungal pathogens causing CFR. However, during the validation phase of the molecular tool, an unidentified fungus was frequently isolated from infected berries. Based on ITS sequences, compared with publicly available sequences, the fungus was identified as belonging to the genus Cadophora. Koch’s postulates confirmed the pathogenicity of the fungus on cranberry fruit. Previously, a Cadophora sp. has been isolated from cranberry fruit in Washington and Oregon but its impact as a factor of CFR appears to be limited. Based on our observations, it was the first most frequently observed fungus on cranberry fruits, which would indicate that it has become an important component of the CFR complex in the Northeast. Specific primers targeting the genus have been developed and the precise specie identification is currently under study. Furthermore, the specific markers are effective when used on samples collected through spore traps. These strategies will be used to monitor the presence and progression of the fungus in cranberry beds to determine if it represents a serious threat for cranberry growers so they can be alerted of the need for preventive treatments.