In Gregarina niphandrodes, an apicomplexan parasite, the sexual stage of its life cycle begins with the association of 2 gamonts. Here, we describe the ultrastructure of the syzygy junction and the nucleus during the transition from unassociated trophozoites to paired gamonts to gamonts in syzygy. Throughout this process, the folds within the syzygy junction undergo changes that correspond to changes of the epicytic folds. The nucleus goes through dramatic changes from multiple spheres of condensed chromatin in unassociated trophozoites, to mostly uncondensed chromatin in paired gamonts, to a large single sphere of condensed chromatin encasing many smaller spheres in gamonts in syzygy. These differing nuclear ultrastructures reflect the dramatic cellular and transcriptional changes associated with life cycle transitions and are indicative of the numerous cell divisions that follow.