Essential oils isolated by using hydrodistillation from the aerial parts of Thymus algeriensis and Thymus capitatus Hoff. et Link. from different locations of Tunisia (Kef, Takelsa, Zaghouan, Fahs and Toukeber) were characterised. The chemical composition was analysed by using gas chromatography/mass spectrometry, the major component of T. capitatus from Kef and T. algeriensis was thymol while carvacrol was the main component of T. capitatus from Zaghouan, Fahs and Toukeber. The antifungal activity of the oils and some pure components was assessed by the in vitro assay against several fungi and oomycetes. T. capitatus (chemotype carvacrol) exhibited the strongest antifungal activity followed by T. capitatus (chemotype thymol) and T. algeriensis, indicating that carvacrol might have a stronger antifungal activity than thymol.