Melaleuca leucadendron Linn is one of Indonesia's most important non-timber forest products as a commercial essential oil. The aim of this research was to identify the variation of compounds in the essential oils of M. leucadendron when leaves were collected at different time from August 2017 to April 2018 at the Yogyakarta Forest Management Unit (FMU). The essential oils were isolated by steam distillation and analyzed by gas chromatography-mass spectrometry (GC-MS). A total of 13 constituents were identified with major compounds, i.e. 1.8-cineole (57.8 to 76.0%), D(+)-limonene (4.40 to 12.1%), p-cymene (1.53 to 12.9%) and α-terpineol (4.98 to 9.98%). The results showed that the weather conditions in the early rainy season, with higher rainfall and flowering, were favorable for the production of essential oil (March) and increased the major compounds, especially from November to January (with the exception of α-terpineol, which was found to be higher in September). In contrast to these main compounds, α-pinene, β-pinene, and humulene are used as marker compounds to distinguish between dry and rainy seasons. In addition, it is also noted that the flowering stage affects the monthly variation of the major compounds.