Polyalkoxybenzenes are plant components displaying a wide range of biological activities. In these studies, we synthesized apiol and dillapiol isoxazoline analogues of combretastatins and evaluated their effect on sea urchin embryos. We have shown that p-methoxyphenyl isoxazoline caused sea urchin embryo immobilization due to the selective excision of motile cilia, whereas long immotile sensory cilia of apical tuft remained intact. This effect was completely reversed by washing the embryos. The compound did not alter cell division, blastulae hatching, and larval morphogenesis. In our hands, the molecule would serve as a convenient tool for in vivo studying morphogenetic processes in the sea urchin embryo. We anticipate that both the assay and the described derivative could be used for studies in ciliary function in embryogenesis.