The adsorption of chitosan onto highly ordered pyrolytic graphite(HOPG) surfaces and its applications have been studied by atomic force microscopy (AFM). The results indicated that chitosan topography formed on the HOPG surface significantly depends on the pH conditions and its concentration for the incubation. Under strongly acidic conditions (pH < 3.5) and at a concentration of 1 mg ml⁻¹, chitosan formed into uniform network structures composed of fine chains. When the solution pH was changed from 3.5 to 6.5, chitosan tends to form a thicker film. Under neutral and basic conditions, chitosan changed into spherical nanoparticles, and their sizes were increased with increasing pH. Dendritic structures have been observed when the chitosan concentration was increased up to 5 mg ml⁻¹. In addition, the chitosan topography can also be influenced by ionic strength and the addition of different metal ions. When 0.1 M metal ions Na+, Mg²+, Ca²+ and Cu²+ were added into the chitosan solution at pH 3.0 for the incubation, network structures, branched chains, block structures and dense networks attached with many small particles were observed, respectively. The potential applications of these chitosan structures on HOPG have been explored. Preliminary results characterized by AFM and XPS indicated that the chitosan network formed on the HOPG surface can be used for AFM lithography, selective adsorption of gold nanoparticles and DNA molecules.