Pea root rot is a major soil-borne disease that threatens global pea production. In this study, diseased pea root samples were collected from Zhejiang Province for pathogen isolation and identification. The mycelial growth rate method was used to evaluate the sensitivity of the pathogens to different fungicides, and transcriptome analysis was performed to investigate the response mechanisms underlying pea root responses to pathogen infection. A total of eight fungal pathogens were identified, including Fusarium solani, F. commune, F. oxysporum, F. proliferatum, F. tricinctum, F. andiyazi, Alternaria alternata, and Didymella pinodella. Among them, F. solani and F. commune were the dominant pathogens. Both pathogens showed high sensitivity to prochloraz, with EC₅₀ values of 0.051 and 0.030 mg·L⁻¹, respectively. Transcriptome sequencing revealed that peas respond to pathogen infection through pathways related to secondary metabolism and plant hormone signal transduction. Furthermore, 14 candidate genes potentially involved in resistance to pea root rot were screened.