The invention belongs to the field of gene sequences and obtaining methods thereof, and particularly relates to a gene sequence a for causing watermelon bisexual flower development and an obtaining method thereof. The gene sequence a has nucleotide base sequences represented by SEQ ID NO:1-6 in the sequence table. The obtaining method comprises the following steps: A, selecting a material for testing, B, extracting genome DNA, C, carrying out a long-distance PCR amplification reaction and detecting the obtained product, D, obtaining a specific amplification sequence, E, obtaining a candidate SNP, and F, verifying the candidate SNP locus, and finally obtaining the gene sequence a for causing watermelon bisexual flower development. According to the present invention, F2 generation segregation population dCAP molecule marker detection and phenotypic identification, and each core germplasm resource dCAP molecule marker detection and phenotypic identification are performed to confirm that the SNP locus is a co-segregation marker; and the obtained SNP locus can be used to develop genetic markers for assisted breeding so as to achieve a purpose of obtaining of the watermelon female line variety.