Meiotic cohesin complexes at centromeres behave differently from those along chromosome arms, but the basis for these differences has remained elusive. The fission yeast cohesin molecule Rec8 largely replaces its mitotic counterpart, Rad21/Scc1, along the entire chromosome during meiosis. Here we show that Rec8 complexes along chromosome arms contain Rec11, whereas those in the vicinity of centromeres have a different partner subunit, Psc3. The arm associated Rec8-Rec11 complexes are critical for meiotic recombination. The Rec8-Psc3 complexes comprise two different types of assemblies. First, pericentromeric Rec8-Psc3 complexes depend on histone methylation-directed heterochromatin for their localization and are required for cohesion during meiosis II. Second, central core Rec8-Psc3 complexes form independently of heterochromatin and are presumably required for establishing monopolar attachment at meiosis I. These findings define distinct modes of assembly and functions for cohesin complexes at different regions along chromosomes.