Limited research has been completed on the root rot complex of common bean (Phaseolus vulgaris L.) in the Caribbean, while yield losses of over 50% due to root rot disease have been reported worldwide. In this study, the predominant root rot pathogens in a 43-year old common bean root rot nursery in Isabela, Puerto Rico, were identified using standard and molecular diagnostic techniques over four planting periods. Evaluations were conducted from Dec. 2009 to Sept. 2012. The most prevalent fungi identified were Fusarium solani, causal agent of Fusarium root rot; Macrophomina phaseolina, causal agent of charcoal rot;and Sclerotium rolfsii, which causes southern blight. Pythium aphanidermathum and Pythium graminicola were also identified during the 2012 evaluation, which cause damping-off and root rot. Other fungi, such as Rhizoctonia solani, were isolated from root and hypocotyl tissue with less frequency. The incidence of the predominant soil-borne pathogens was largely correlated across seasons. Low nitrogen levels in the soil,and low nitrogen,phosphorus,potassium,and magnesium in leaf tissue were identified in the nursery and have been achieved through no application of fertilizer. Knowledge of the prevalence of soil borne pathogens and fertility conditions will be used for targeting the selection of breeding materials at the Isabela root rot nursery and in other testing locations.