Bisphenol A (BPA), which is widely used for manufacturing polycarbonate plastics and epoxy resins, has been banned from use in plastic baby bottles because of concerns regarding endocrine disruption. Substances with similar chemical structures have been used as BPA alternatives; however, limited information is available on their toxic effects. In the present study, we reviewed the endocrine disrupting potential in the gonad and thyroid endocrine system in zebrafish after exposure to BPA and its alternatives (i.e., bisphenol AF, bisphenol C, bisphenol F, bisphenol S, bisphenol SIP, and bisphenol Z). Most BPA alternatives disturbed the endocrine system by altering the levels of genes and hormones involved in reproduction, development, and growth in zebrafish. Changes in gene expression related to steroidogenesis and sex hormone production were more prevalent in males than in females. Vitellogenin, an egg yolk precursor produced in females, was also detected in males, confirming that it could induce estrogenicity. Exposure to bisphenols in the parental generation induced a decrease in the hatchability associated with offspring generation. In zebrafish exposed to bisphenols, significant decreases in thyroxine concentrations and increases in thyroid-stimulating hormone concentrations were commonly observed. Alternative compounds used to replace a chemical of concern are believed to be less toxic than the original compound; however, several BPA alternatives appear to have similar or greater effects on the endocrine system in zebrafish. Since endocrine systems interact with each other, further studies are needed to assess the primary target of BPA alternatives among the endocrine axes.