Hydroxyapatite (HAp) and bacterial cellulose (BC) are both excellent materials for use in biomaterial areas. The former has outstanding osteoconductivity and bioactivity and the latter is a high-strength nano-fibrous and extensively used biomaterial. In this work, the HAp/BC nanocomposites with a 3-dimensional (3-D) network were synthesized via a biological route by soaking both phosphorylated and unphosphorylated BCs in 1.5 simulated body fluid (SBF). Scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transformed infrared spectroscopy (FTIR), and transmission electron microscopy (TEM) were employed to characterize the HAp/BC nanocomposites. SEM observations demonstrated that HAp crystals were uniformly formed on the phosphorylated BC fibers after soaking in 1.5 SBF whereas little Hap was observed on individual unphosphorylated BC fibers. Our experimental results suggested that the unphosphorylated BC did not induce Hap growth and that phosphorylation effectively triggered HAp formation on BC. Mechanisms were proposed for the explanation of the experimental observations. XRD and FTIR results revealed that the HAp crystals formed on the phosphorylated BC fibers were carbonate-containing with nanosized crystallites and crystallinities less than 1%. These structural features were close to those of biological apatites.