Pichia pastoris is a methylotrophic yeast that is widely used for the expression of heterologous proteins. Here, we have investigated the dependence of AOX1 and CAT1 expression on the source of nitrogen. It has shown that the expression of AOX1 and CAT1 depends on the source of nitrogen. In the presence of a rich nitrogen source, such as glutamine or ammonium sulfate, the AOX1 and CAT1 expression was dramatically induced. With proline as the nitrogen source AOX1 and CATI expression was reduced by more than threefold. The expression of these genes is controlled at the level of transcription. We have shown the impact of the nitrogen source on the growth rate in the presence of methanol as a sole carbon source. The specific growth rate was highest on media that contained proline as a nitrogen source compared to media with a rich nitrogen source.