The Rodalquilar epithermal gold alunite deposit occurs within the Rodalquilar caldera complex, in the Cabo de Gata volcanic field, a semi‐arid region in southeast Spain. The epithermal mineralization is associated with an extensive east–west trending zone of hydrothermally altered rocks. The presence of several short‐wave infrared (SWIR) active minerals in the hydrothermal alteration assemblage makes an investigation of the spatial distribution of the hydrothermal alteration mineralogy using remote sensing imagery possible. Multiple Endmember Spectral Mixture Analysis (MESMA) was applied to analyse SWIR imaging spectrometer data recorded by the HyMap imaging system, in order to map surface mineralogy in the Rodalquilar caldera. A nine endmember set derived from the imagery was used. The MESMA was based on models of two up to five endmembers assessed in terms of fraction and root‐mean‐square‐error criteria. MESMA allowed identification of short‐wave infrared active surface mineralogy and resolved the mixed spectral response from the surface mineralogy and vegetation cover. Field spectral measurements were also used to verify the mineral maps. The results of this study have potential to refine the map of the hydrothermal alteration zones in the Rodalquilar caldera complex. The study demonstrates that MESMA is an effective unmixing technique in geological applications of imaging spectrometry in semi‐arid regions.