Ciliopathies refer to a genetically and clinically heterogeneous class of disorders that result from defects in the formation or function of the primary cilium. Cilia are the microtubule-based organelles that protrude from the surface of almost all vertebrate cells, including the rod and cone photoreceptors. The photoreceptor sensory cilium consists of the connecting cilium and outer segment with the outer segment forming a unique structure containing thousands of tightly packed disc membranes. Mutations in over 50 genes result in syndromic ciliopathies that can manifest with retinal degeneration, including Bardet-Biedl syndrome (BBS), Joubert Syndrome, Jeune Syndrome, and nephronophthisis (NPHP) or in non-syndromic retinal dystrophies like Leber Congenital Amaurosis (LCA) and Retinitis Pigmentosa (RP). Zebrafish have been widely used as a model system to study ciliopathies, particularly BBS and Joubert Syndrome, and for studying the mechanisms leading to photoreceptor degeneration associated with these disorders. Investigators were drawn to zebrafish due to the rapid growth and transparency of the zebrafish embryo, the differentiation of photoreceptors by 3 days post-fertilization, and the ability to suppress gene function through morpholino knockdown. The genetic heterogeneity of ciliopathies and desire for more accurate genotype-phenotype correlations make zebrafish an appealing model for studying gene- and allele-specific differences in a rapid manner. This review will discuss the current zebrafish models of retinal ciliopathies, evaluate the widespread use of morpholinos as tools to knock down gene function in zebrafish, and make predictions on how zebrafish will contribute in future studies of ciliopathies.