In order to clarify the SFB gene diversity in Malus and the distribution frequency of each sequence haplotype in ecological populations, 82 Malus germplasm resources including the cultivated apples (i.e. Kuihua) and wild resources (i.e. Malus sieversii (Led.) Roem.) were used. The genotyping was conducted using three gene-specific primer combinations. PCR amplification using leaf DNA produced a single SFB gene fragment in all materials. Sanger sequencing of PCR products revealed five haplotypes of the SFB gene, corresponding SFB1, SFB2, SFB3, SFB7and SFB9 based on GenBank homology comparison. At the same time, the distribution frequency of SFB gene in different ecological population was analyzed. The frequencies of different haplotypes in populations were different, and the highest frequency of SFB3 was 45.12 %, followed by SFB1 (42.60 %). The intraspecific and interspecific frequency of the same SFB gene was also different. In addition, the phylogenetic tree analysis showed that Malus sieversii (Led.) Roem was related to the domestication and origin of Malus trukmenorum (Juz, et Pop.) Likh. and apple cultivars.