This study evaluated the follicular atresia, cell proliferation, and anti-Mullerian hormone action in Aotus nancymae and Sapajus macrocephalus during three sexual phases (follicular, luteal, and gestational). Follicular quantification and immunolocalization of Caspase-3 protein, B-cell lymphoma 2 (BCL-2), proliferating cell nuclear antigen (PCNA), and anti-Mullerian hormone (AMH) were performed. A significant difference in the quantification between preantral and antral follicles, with a progressive decrease in the antrals, was identified. Protein and hormonal markers varied significantly between follicle cell types (A. nancymae p = 0.001; S. macrocephalus, p = 0.002). Immunostaining in the preantral and antral follicles was present in all sexual phases; for Caspase-3, in granulosa cells, oocytes, and stroma; for BCL-2, in granulosa cells, oocytes, and theca; and for PCNA and AMH, in oocytes and granulosa cells. The immunostaining for Caspase-3 was more expressive in the preantral follicles (follicular phase, p < 0.05), while that for BCL-2 and PCNA was more expressive in the antral follicles of the follicular phase. The AMH was more expressive in the primary and antral follicles of nonpregnant females, in both the follicular and luteal phases. Our results contribute to understanding the ovarian follicular selection, recruitment, and degeneration of these species.