Abstract <p>Fish caudal fin is a complex multifunctional system with a long evolutionary history involving a series of fusions and losses of posterior vertebrae and associated elements. Among the different methods used to elucidate the evolutionary transformations of the caudal fin and the homology of its constituent elements, experimental heterochronies seem to be a promising approach. Here, we present the experimental results of alterations of temporal developmental characteristics induced by hypothyroidism in zebrafish <i>Danio rerio</i> (Danionidae), a model fish that is actively used object in the studies of heterochronies. We revealed a high variability in the caudal fin skeleton: most structures are characterized by two or more normal states in both the euthyroid and hypothyroid zebrafish. This finding suggests that these structures are not tightly developmentally constrained and may follow different developmental trajectories. Hypothyroidism significantly increases both the developmental and phenotypic variability of skeletal structures, induces skewness of the frequency distribution of typical feature states and the appearance of traits that are nonspecific to zebrafish but inherent to other, even phylogenetically distant, taxa, demonstrating experimental atavisms. Hypothyroidism-induced heterochronies are temporally-, spatially-, and individual-specific and have a wide range of phenotypic consequences. The absence of severe morphological disorders and no visible deterioration of swimming indicate that experimental heterochronies induced in our research lead to morphological changes that remain integrated and patterned into the caudal fin complex. A thorough analysis of the experimental heterochronies and their phenotypic consequences allows elucidating the developmental pathways, composition, evolutionary transformations and homologies of the skeletal elements composing a skeleton of the caudal fin.</p>