The chemical composition of Hyssopus officinalis (Lamiaceae) essential oil grown in southeastern Spain was analyzed by GC-MS. Due to the high relevance of this species in the world market, the study is focused on chemical heterogeneity of different oil batches and their extraction yield, cultivated under irrigation and non-irrigation conditions and with different harvesting dates. All essential oil samples have two main terpene compounds which are pinocamphone and iso-pinocamphone, accounting for approximately 35–40% of the total oil content. Other relevant compounds were identified, with β-pinene, which accounted for 10–17% contribution to the total composition, standing out. Significant differences between their volatile composition have been observed between treatments, being limonene, (E)-β-ocimene, pinocarveol, α-pinene and β-phellandrene the compounds that contributed most to the discrimination. It was also observed that the irrigation period is the most favourable for the cultivation of hyssop in this region, specially for batch 7 which gives the highest extraction yield and the best EO quality.