Gene–centromere mapping using half-tetrad analysis is a powerful tool for understanding chromosomal behaviour and determining the position of centromeres in relation to genes or markers in fish. In this study, eight gynogenetic diploid families induced by inhibiting of the second meiotic division were genotyped at 66 microsatellite loci for microsatellite–centromere (M-C) mapping in bighead carp ( Aristichthys nobilis). The absence of paternal alleles verified the success of gynogenetic development in all gynogenetic families. All loci were consistent with Mendelian segregation in control families. The estimated recombination frequency (y) ranged from 0.057 to 0.875 with an average of 0.477 ± 0.222. Seventeen loci (25.76%) showed high M-C recombination frequencies of over 0.667. M-C distances ranged from 2.85 to 43.75 cM under the assumption of complete interference. Thus, these loci are distributed from the centromeres to the telomeres of their respective chromosomes, while mainly in the intermediate region. Information on centromere mapping could serve as a starting point to consolidate the genetic linkage groups in bighead carp.