Summary Rationale Recombination suppression in sex chromosomes and mating type loci can lead to degeneration due to reduced selection efficacy and Muller’s ratchet effects. However, genetic exchange in the form of non-crossover gene conversions may still take place within crossover-suppressed regions. Recent work has found evidence that gene conversion may explain the low levels of allelic differentiation in the dimorphic mating type locus ( MT ) of the isogamous alga Chlamydomonas reinhardtii . However, no one has tested whether gene conversion is sufficient to avoid the degeneration of functional sequence within MT . Methods Here, we calculate levels of linkage disequilibrium (LD) across MT as a proxy for recombination rate and investigate its relationship to patterns of population genetic variation and the efficacy of selection in the region. Results We find that levels of LD predict selection efficacy across MT , and that purifying selection is stronger in shared genes than MT -limited genes to the point of being equivalent to that of autosomal genes. Conclusions We argue that isogamous systems without secondary sexual characteristics exhibit reduced selective pressure to differentiate sex chromosomes, and that recombination via gene conversion plays an important role in both reducing differentiation and preventing degeneration of crossover suppressed mating type loci.