In this study, the characterization of the optical properties of natural hydroxyapatite (HAp) [Ca10(PO4)6(OH)2] is discussed. In the first stage of the experiment, natural HAp was processed from the bones of Brazilian river fish such as pintado (Pseudoplatystoma corruscans), jaú (Paulicea lutkeni), and cachara (Pseudoplatystoma fasciatum). The bones were calcined at 900°C for different amounts of time (4–12h) and reduced to powder using two different milling times (2 and 4h) in a high-energy ball mill, in order to determine the best procedure for obtaining natural nanostructured HAp powder for the study. In the second stage, material calcined for 8h was milled for 2, 4, 8, and 16h. The techniques of photoacoustic spectroscopy, scanning electron microscopy, and flame atomic absorption spectrometry were applied to characterize these samples. The O–H stretching shown by photoacoustic spectroscopy was correlated to the HAp nanostructure. Structural analysis indicated a Ca∕P ratio close to 1.67 (∼1.64±0.04) and the presence of morphology and particle phase structure in the nanostructured HAp powder.