The industrial filleting of blue shark (Prionace glauca) led to the generation of a large number of central skeletons of low interest to fishmeal plants handling such wastes. In this context, the present study describes the optimization of the hydrolysis process (pH 8.35, T 58 °C, 1% (v/w) of alcalase and t = 4 h) to produce chondroitin sulfate (CS) together with the recovery of bioapatites. Then, that hydrolysate was chemically treated with an optimal alkaline-hydroalcoholic-saline solution (0.48 M of NaOH, 1.07 volumes of EtOH and 2.5 g/L of NaCl) and finally purified by ultrafiltration-diafiltration (30 kDa) to obtain glycosaminoglycan with a purity of 97% and a productive yield of 2.8% (w/w of skeleton). The size of the biopolymer (CS) was of 58 kDa with prevalence of 6S-GalNAc sulfation (4S/6S ratio of 0.25), 12% of GlcA 2S-GalNAc 6S and 6% of non-sulfated disaccharides. Crude bioapatites were purified by pyrolysis and FT-Raman and XRD techniques confirm the presence of hydroxyapatite [Ca5(PO4)3(OH)], with a molar mass of 502.3 g/mol, embedded in the organic matrix of the skeleton. The mineralized tissues of blue shark are promising marine sources for the extraction of high value biomaterials with clinical application in bone and tissue regeneration and are still completely unexplored.