Gonad development in zebrafish is not well understood. Primordial germ cells, undifferentiated and bi-potential, differentiate into oogonia during early larval development. Thereafter, testicular ontogenesis is initiated through the development of immature oocytes. The primary signal of testicular differentiation remains a mystery. The aim of the research reported in this article was to identify biomarkers for the detection of impending sex inversion in zebrafish. The terminal deoxynucleotidyl transferase mediated dUTP nick end labelling (TUNEL) technique was used to predict impending juvenile sex inversion. Results indicate the presence of TUNEL-positive cells in juvenile and adult ovaries. In juvenile ovaries, ‘growing’ areas revealed intense positive labelling, while in adult ovaries, positive signals were restricted to the nuclei of epithelial/thecal cells, post-pachytene and pre-vitellogenic oocytes. Further, the present research indicated that some forms of non-apoptotic DNA fragmentation were labelled by the TUNEL assay. The present results support the notion of the possible involvement of apoptosis in normal ovarian growth, but do not appear to be restricted to the period prior to and during juvenile testicular ontogenesis. Whether the TUNEL-positive labelling seen here was indicative of DNA fragmentation or not could not be determined with certainty. The TUNEL assay is, therefore, not a suitable and sensitive marker for predicting impending sex inversion in zebrafish. However, further comparative studies using other biochemical and immunohistochemical studies will be needed to confirm current research findings. Identifying instructive and trophic molecules and their stage specific roles in regulating normal development may help elucidate important principles controlling germ cell differentiation.