A comparative study of the microscopic morphology and chemical characteristics of spicules of Hexactinellids (Hexactinellida) with different structural features of the skeletons, as well as the freshwater Baikal sponge belonging to the class of common sponges (Demospongia), was carried out. The trace element composition of sponge spicules was determined by X-ray fluorescence spectrometry. The spicules of siliceous sponges contain many elements, arranged in decreasing order of concentration: Si, Ca, Fe, Cl, K, Zn, and others. It was shown that the surface layer of sea sponges contains mainly carbon (C), oxygen (O), and to a lesser extent nitrogen (N), silicon (Si), and sodium (Na). The spicules of the studied siliceous sponges can be divided into two groups according to the phase composition, namely one containing crystalline calcium compounds and one without them. Analysis of infrared absorption spectra allows us to conclude that the sponges Euplectella aspergillum, E. suberia and Dactylocalyx sp. contain silica partially bound to the organic matrix, while the silica skeleton of the sponges of the other group (Schulzeviella gigas, Sericolophus sp., Asconema setubalense, Sarostegia oculata, Farrea sp. and Lubomirskia baicalensis sp.) practically does not differ from the precipitated SiO₂. This comparative study of the chemical composition of the skeletons of marine Hexactinellids and common freshwater sponge allows us to conclude that there are no fundamental differences in the chemical composition of spicules, and all of them can be used as a starting material for creating new composite silicon–organic functional materials.