The invention belongs to the field of citrus genomics and discloses a co-dominance InDel molecular marker for identifying single embryo and multiple embryos of citrus and application thereof. By carrying out depth re-sequencing on whole genome DNA of 107 materials including tangelos and oranges, whole genome sequence information is obtained, by means of comparing and screening, the gene sequence information in single-embryo and multi-embryo candidate areas is obtained, the sequence with the highest relevance degree to phenotype is screened out, and the sequence is an InDel sequence of 6bp. Accordingly, a set of simple, fast and co-dominant PCR markers are developed, and primers are used for carrying out PCR amplification on CK F/R, INS F/R and DEL F/R, so that the co-dominance InDel molecular marker for identifying the single embryo and the multiple embryos of the citrus is obtained. Finally, the marker is utilized for testing loci in 115 single-plant natural groups and 100 single-plant hybridized groups. The marker has the biggest advantages that cost is low, accuracy is high, and embryonic early selection can be achieved during the citrus seedling stage.