SummaryMeiotic chromosomes organize around a cohesin-dependent axial element, which promotes meiotic recombination and fertility. In the absence of cohesin, axial-element proteins instead accumulate in poorly understood genomic regions. Here, we show in S. cerevisiae that these regions are particularly enriched for axis proteins even on wild-type chromosomes and thus reflect a cohesin-independent recruitment mechanism. By contrast, other organizers of chromosome structure, including cohesin, condensin, and topoisomerases, are depleted from the same regions. This spatial patterning is observable before meiotic entry and therefore independent of meiotic recombination. Indeed, the regional density of gene-coding sequences is sufficient to predict a large fraction of cohesin-independent axis protein binding, suggesting that the gene-associated chromatin landscape plays a role in modulating axis protein deposition. The increased accumulation of axis proteins in these regions corresponds to a greater potential for initiation of recombination and progression to crossovers.