This dataset contains scanning electron microscopy (SEM) images of sponge spicules from three individuals of the glass sponge Anoxycalyx (Scolymastra) joubini (Topsent, 1916), collected in McMurdo Sound, Ross Sea, Antarctica. The sponge samples were obtained by scientific divers during the SpongeScan expedition in October and November 2024 to support morphological characterization and taxonomic classification of the species. To ensure representative sampling, each approximately 70 cm high sponge was biopsied at five different heights using a metal coring tube. The collected tissue samples were immediately flash-frozen in liquid nitrogen. In the laboratory, aprox. 1cm3 thawed tissue was treated with sodium hypochlorite (10%) at room temperature to dissolve organic material while leaving behind the siliceous spicules. The latter were then washed multiple times with distilled water until neutral pH was reached, followed by a graded ethanol dehydration series (30%, 50%, 70%, 90%, and 100%). After final ethanol washes, the spicules were transferred onto SEM object holders with carbon adhesive, dried at 50 °C, and sputter-coated with gold. Prior to SEM imaging, light microscopy was used to verify the absence of organic residues.