The present study investigated autophagic processes in Danio rerio preovulatory follicles (Stage III and IV). There were more autophagosomes, as revealed by electron microscopy, in follicles from females fed the probiotic Lactobacillus rhamnosus IMC 501. This was confirmed by increased expression of genes involved in the autophagic process, namely ambra1, becn1, lc3 and uvrag. In addition, preovulatory follicles from females fed the probiotic contained more microtubule-associated protein 1 light chain 3 isoform II (LC3-II) and less p62 protein. The increased autophagy in preovulatory follicles from females fed the probiotic was concomitant with a decrease in the apoptotic process in the ovary, as evidenced by terminal deoxyribonucleotidyl transferase-mediated dUTP-digoxigenin nick end-labelling analysis and confirmed by lower expression of genes involved in apoptosis (i.e., p53, bax, apaf and cas3) and higher expression as igfII and igf1r. The results of the present study provide preliminary evidence of the involvement of autophagy during follicle development in the zebrafish ovary. In addition, we have demonstrated for the first time that a functional food, such as L. rhamnosus IMC 501, can modulate the balance between apoptosis and autophagy that regulates ovary physiology in zebrafish by inhibiting follicular apoptosis and improving follicular survival.