Saccharomyces cerevisiae Mek1 is a CHK2/Rad53-family kinase that regulates meiotic recombination and progression upon its activation in response to DNA double-strand breaks (DSBs). The full catalog of direct Mek1 phosphorylation targets remains unknown. Here, we show that phosphorylation of histone H3 on threonine 11 (H3 T11ph) is induced by meiotic DSBs in S. cerevisiae and Schizosaccharomyces pombe. Molecular genetic experiments in S. cerevisiae confirmed that Mek1 is required for H3 T11ph and revealed that phosphorylation is rapidly reversed when Mek1 kinase is no longer active. Reconstituting histone phosphorylation in vitro with recombinant protein demonstrated that Mek1 directly catalyzes H3 T11ph. Mutating H3 T11 to nonphosphorylatable residues conferred no detectable defects in otherwise unperturbed meiosis, although the mutations modestly reduced spore viability in certain strains where Rad51 is used for strand exchange in place of Dmc1. H3 T11ph is therefore mostly dispensable for Mek1 function. Despite its minimal role, however, H3 T11ph is an excellent candidate for a marker of ongoing Mek1 kinase activity in vivo. We therefore used anti-H3 T11ph chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) to examine the genome-wide spatial disposition of Mek1 kinase activity. H3 T11ph was highly enriched at presumed sites of attachment of chromatin to chromosome axes, and also gave a weaker signal that was highly localized at hotspots for DSB formation. These findings indicate that Mek1 provides functional communication between axes and the sites where recombination is occurring, thus providing insight into the higher order organization of recombining meiotic chromosomes.