The invention discloses a molecular marker for identifying homozygous or heterozygous types of eriobotrya japonic lindl yellow-flesh character genes and application of the molecular marker. When a variety of an eriobotrya japonic lindl yellow flesh character gene type is homozygous, a nucleotide sequence of the molecular marker is as shown in SEQ ID NO. 1; when the variety of the eriobotrya japonic lindl yellow flesh character gene type is heterozygous, a nucleotide sequence of the molecular marker is as shown in SEQ ID NO. 1-2. Through the molecular marker, the variety of the eriobotrya japonic lindl yellow-flesh character gene types can be accurately identified in advance. For the breeding of a new variety of white-flesh eriobotrya japonic lindl, a heterozygous type and a heterozygous type can be selected or the heterozygous type is hybridized with the white-flesh type during the selection and mating of cross parents, and the white-flesh character must appear in filial generation groups, and the new variety of white-flesh eriobotrya japonic lindl may be obtained, the breeding efficiency is improved, and the breeding cost is reduced.