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We have constructed a chromosome-specific cosmid library from electrophoretically separated chromosomes of the basidiomycete Coprinus cinereus and performed contig mapping and analysis of chromosome length polymorphisms (CLPs) for the smallest chromosome of the 5302 strain. A contig map of about 300kb indicated that the novel size chromosomes in the F 1 progeny were apparently recombinants containing physical markers derived from both ends and central regions in this map. This may be the first case in which the formation of CLPs in the F 1 generation has been explained using the contig map. The results obtained were consistent with the hypothesis that novel CLPs were produced by meiotic recombination between the parental homologous chromosomes of unequal sizes.