BACKGROUND: Many single‐nucleotide polymorphisms have been identified in the coding region of the FUT2 locus, which encodes secretor type α(1,2)fucosyltransferase. In addition, three recombination alleles have been reported. Of these recombination alleles, a fusion gene generated by an unequal crossing over between Sec1, a pseudogene that locates 23 kb upstream to and has high sequence homology with FUT2 and FUT2, was identified as a Japanese‐specific nonsecretor allele (sefus).STUDY DESIGN AND METHODS: During the screening of the sefus in Mongolians (n = 118), a hybrid allele of Sec1‐FUT2‐Sec1 was found.RESULTS: The DNA sequence suggested that the Sec1‐FUT2‐Sec1 allele contains a 275‐bp sequence (between positions 259 and 533) that is identical to the FUT2 sequence including a 54‐bp FUT2‐specific region (between positions 417 and 470) and that might have been generated by an interlocus gene conversion.CONCLUSION: Because the recombination region of sefus and the upstream recombination region of Sec1‐FUT2‐Sec1 are almost identical, this sequence stretch is likely to be the breakpoint for different kinds of recombinations that occur in this family of genes.