Salmon cartilage proteoglycan fractions have recently gained favor as ingredients of functional food and cosmetics. An optimal hot water method to extract proteoglycan from salmon cartilage has recently been developed. The extracted cartilage includes hyaluronan and collagen in addition to proteoglycan as counterparts that interact with each other. In this study, biochemical analyses and atomic force microscopical analysis revealed global molecular images of proteoglycan in the hot water extract. More than seventy percent of proteoglycans in this extract maintained their whole native structures. Hyaluronan purified from the hot water extract showed a distribution with high molecular weight similar to hyaluronan considered to be native hyaluronan in cartilage. The current data is evidence of the quality of this hot water cartilage extract.