The ultrastructure of isolated fibrils of Chondrosia reniformis sponge collagen was investigated by collecting characteristic data, such as fibril thickness, width, D-band periodicity, and height modulation, using atomic force microscopy (AFM) and transmission electron microscopy (TEM). Therefore an adapted pre-processing of the insoluble collagen into homogeneous suspensions using neutral buffer solutions was essential, and several purification steps have been developed. Fourier transform infrared reflection-absorption spectroscopy (FT-IRAS) of the purified sponge collagen showed remarkable analogy of peak positions and intensities with the spectra of fibrillar calf skin type I collagen, despite the diverse phylogenetic and evolutionary origin. The sponge collagen's morphology is compared with that of other fibrillar collagens, and the typical banding of the separated single fibrils is discussed by comparison of topographical data obtained using AFM and corresponding TEM investigations using common staining methods. As the TEM images of the negatively stained fibrils showed alternating dark and light bands, AFM revealed a characteristic periodicity of protrusions (overlap zones) followed by two equal interband regions (gap zones). AFM and TEM results were correlated and multiperiodicity in Chondrosia collagen's banding is demonstrated. The periodic dark bands observed in TEM images correspond directly to the periodic protrusions seen by AFM. As a result, we provide an improved, updated model of the collagen's structure and organization.