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Across the teleost skeleton, cartilages are diverse in their composition suggesting subtle differences in their developmental mechanisms. This study aims to elucidate the regulatory role of bone morphogenetic protein (BMPs) during the morphogenesis of two cartilage elements in zebrafish: the scleral cartilage in the eye and the caudal fin endoskeleton. Zebrafish larvae were exposed to a BMP inhibitor (LDN193189) at a series of timepoints preceding the initial appearance of the scleral cartilage and caudal fin endoskeleton. Morphological assessments of the cartilages in later stages, revealed that BMP‐inhibited fish harbored striking disruptions in caudal fin endoskeletal morphology, regardless of the age at which the inhibitor treatment was performed. In contrast, scleral cartilage morphology was unaffected in all age groups. Morphometric and principal component analysis, performed on the caudal fin endoskeleton, revealed differential clustering of principal components one and two in BMP‐inhibited and control fish. Additionally, the expression of sox9a and sox9b were reduced in BMP‐inhibited fish when compared to controls, indicating that LDN193189 acts via a Sox9‐dependent pathway. Further examination of notochord flexion also revealed a disruptive effect of BMP inhibition on this process. This study provides a detailed characterization of the effects of BMP inhibition via LDN193189 on zebrafish cartilage morphogenesis and development. It highlights the specific, localized role of the BMP‐signaling pathways during the development of different cartilage elements and sheds some light on the morphological characteristics of fossil teleosts that together suggest an uncoupling of the developmental processes between the upper and lower lobes of the caudal fin. Research Highlights: Treatment of zebrafish larvae with LDN193189, a bone morphogenetic protein inhibitor, caused severe morphological disruptions in caudal fin cartilage but spared the scleral cartilage.Expression of sox9a/b was reduced during the early development of caudal fin cartilage after LDN193189 treatment compared to controls.Dorsal flexion of the notochord was disrupted in zebrafish treated with LDN193189. [ABSTRACT FROM AUTHOR]