Vertebrate cartilage development requires a tight regulation to ensure the proper differentiation and morphology of various cartilaginous elements. The bone morphogenetic protein (BMP) signaling pathway is highly involved in regulating cartilage morphogenesis. In this study, zebrafish larvae were exposed to a pharmaceutical BMP inhibitor, LDN193189, prior to the development of two cartilage structures: the scleral cartilage and the caudal fin endoskeleton. BMP inhibition had no effect on the scleral cartilage, while severe morphological disruptions were apparent in the caudal fin, as determined via wholemount bone and cartilage staining. The disrupted fin cartilage phenotype was characterized and quantified using morphometric techniques and principal component analysis. Using in-situ hybridization, we further confirmed that BMP inhibition caused a reduced expression of sox9, a well-known cartilage development master regulator. This study is one of the first to utilize LDN193189 to study zebrafish cartilage development, and our results shine a light on the different regulatory systems at play in the development of different cartilage elements. Additionally, this study adds to our knowledge of caudal fin development and evolution.