Salmon bones - byproducts in food industries, was regarded as waste and will be discarded without fully utilizing it. From the approach of waste to wealth in the chemical compositions, the by-product can be employed as a cheap bioresource to form nanohydroxyapatite. In this paper, the influence of hydrothermal and calcined conditions on the structure of nano-hydroxyapatite synthesized from the salmon fishbone by the hydrothermal method was investigated. Various techniques such as X-ray diffraction (XRD), Fourier-transform infrared (FTIR) spectroscopy, field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), and X-ray fluorescence spectrometry (XRF) were used to characterize the samples. XRD studies revealed that hydrothermal and calcined conditions affected the crystallinity as well as the purity of the hydroxyapatite. The suitable conditions for the synthesis of nanohydroxyapatite were proposed such as the hydrothermal at 120 °C for 8 hrs and calcined at 800 °C for 2 hrs. At the conditions, the hydroxyapatite had a spherical shape with the nanoparticle size in a range of 30–60 nm, and reached a BET surface area of 13.8 m2.g−1, a pore volume of 0.018 cm3.g−1, and a pore diameter of 24.8 Å. The molar ratio of Ca/P in the hydroxyapatite was 1.64, which is the ratio one would expect for hydroxyapatite.