The invention relates to a method for obtaining a capsicum phytophthora resistance candidate gene and a molecular marker, and application. The method is used for obtaining the capsicum phytophthora resistance candidate gene by utilizing capsicum phytophthora transcriptome and whole-genome sequencing data information, differentially-expressed gene identification, bioinformatics analysis, molecular marker development and phytophthora inoculation identification and belongs to the technical field of capsicum biology. The method comprises the following steps: sequencing a phytophthora resistant and susceptible gene pool transcriptome obtained after phytophthora inoculation of an F2 population constructed by capsicum highly-resistant and highly-susceptible phytophthora materials, performing expression analysis and functional annotation on differential genes, extracting DNAs (Desoxvribose Nucleic Acid) of a capsicum phytophthora highly-resistant and highly-susceptible phytophthora material genome, performing primer design and PCR (Polymerase Chain Reaction) amplification, performing sequence difference analysis and SNP site identification, performing SNP specific primer design and validity verification, and performing other steps to efficiently obtain the capsicum phytophthora resistance candidate gene and the molecular marker. According to the method, the capsicum phytophthora resistance candidate gene can be accurately identified, and the effective molecular marker can be developed.