The St Lawrence ST74-OR23-IVA and Lindegren Y8743 strains of Neurospora crassa have a different provenance from wild collections and dissimilar cog alleles; that in Lindegren, cogLa (previously designated cog+), is a more efficient recombinator than cogS74A and cogEa (previously cog), the alleles in St Lawrence and Emerson a respectively. Restriction fragment length polymorphisms (RFLPs) and sequence polymorphisms (SPs) were used to map the difference between cogLa and cogS74A to a region that extends from 2.3 to 3.2 kb 3' of the his-3 coding sequence. The DNA sequences from 400 bp 3' of his-3 to 120 bp 3' of the cog region in these strains were found to be homologous but to diverge by 3.5%. The differences include single-base pair changes, short insertion/deletions, differences in the length of poly-T tracts, and three longer sequences present only in St Lawrence: a 98-bp inverted repeat transposable element we have previously called Guest, which has generated a 3-bp direct repeat of the target site present in Lindegren, and 15-bp and 20-bp sequences that have no obvious structural features nor similarity to Guest. Southern analysis of other laboratory strains revealed four major and several minor variants of this region. All strains assayed are descendants of Lindegren A, Lindegren a, Abbott 4A and Abbott 12a, and it is clear that each of these progenitors collected from the wild population had a different variant of the cog region. Sequence divergence of this degree seems remarkable, even in an intergenic region, for fully interfertile strains of a single species.