The Ga2 locus controls unilateral cross incompatibility in Zea species. Molecular characterization of this locus indicates that fully functional loci contain two components that function in male and female reproductive tissues, Ga2P and Ga2F respectively. Some Zea mays varieties have been reported to be capable of overcoming the Ga2 reproductive barrier including the widely used inbred line Mo17. Our objective was to better understand the structure, function and distribution of the Ga2 locus in Zea species. To do this, we first examined the ability to overcome the Ga2 reproductive barrier across a diverse sample of Zea mays inbred lines. The ability of Mo17 to overcome the Ga2 reproductive barrier was mapped to the Ga2 locus. We next examined the structure of the Ga2 locus. Like the Ga1 locus, the Ga2 locus in Zea mays sp. contains multiple repeated functional genes and pseudogenes encoding the Ga2P and Ga2F pectin methylesterase enzymes. The organization of these repeat units is similar in the three sweet corn lines examined, and all are capable of overcoming the reproductive barrier. The non-sweet corn lines have a variety of genome structures, but these structures do not correlate well with the ability to overcome the Ga2 reproductive barrier. Levels of transcripts derived from Ga2P and the ability to overcome the reproductive barrier in sweet corn are higher in sweet corn lines than the other lines tested. The role of Ga2P in Zea mays in the apparent absence of a functional female factor remains unclear and may be evidence for an additional role in reproductive tissues.