We present the results of studying the structure of gold nanoparticles synthesized on the silicon surface by two techniques: pulsed laser ablation and magnetron sputtering. The surface morphology is examined by scanning electron microscopy. The structure of the obtained gold nanoparticles is analyzed by transmission electron microscopy and electron diffraction. It is shown that nanoparticle sizes and crystal structures can be controlled by their thermal annealing. Mechanisms occurring during annealing of thin gold films and also their effect on the formation of nanoparticles with different structures are investigated.