This study investigates the ecological niches and projected climate-driven distributional shifts of two endemic Moroccan species, Origanum compactum and Origanum elongatum, both of high ecological and socio-economic importance. The purpose was to characterize their current distribution, identify the key climatic variables structuring their ecological niches, and forecast changes under a severe climate scenario (SSP5-8.5, 2061–2080) to assess vulnerability and inform conservation strategies. An ecological niche modeling framework was applied using occurrence data from published sources and GBIF, combined with six bioclimatic predictors. Multiple algorithms (GLM, GBM, ANN, RF, and MAXENT) were evaluated, with high-performing models (AUC > 0.9, TSS > 0.8) integrated into ensemble projections. Niche overlap was quantified through Schoener’s D index and further tested with equivalency and similarity analyses. Results revealed marked ecological differentiation between the two species (D = 0.2; p = 0.001), with O. compactum associated with moderately warm, precipitation-sensitive environments and O. elongatum showing broader tolerance to temperature and aridity gradients. Projections indicated a drastic reduction in highly suitable habitats for both taxa, with O. compactum declining by 87% (from 4,980 to 626 km²) and O. elongatum by 89% (from 3,688 to 407 km²). Although moderately and low-suitability zones expanded substantially, these marginal habitats may not fully compensate for the loss of optimal environments. The study, while limited to climatic predictors, without incorporating anthropogenic pressures, highlights clear conservation priorities: safeguarding residual core habitats for O. compactum and maintaining ecological connectivity for O. elongatum. It provides original insights into the contrasting adaptive capacities of Mediterranean endemics under climate change. Importantly, this is the first comparative niche analysis of these two endemic Origanum species in northern Morocco that integrates niche-equivalency testing with forward climate projections, offering actionable and spatially explicit guidance for biodiversity conservation and the sustainable management of medicinal plants.