The variability of the volatile profile of 70 propolis samples from acaricide-treated and -untreated beehives maintained at Algarve (Portugal) was evaluated. Propolis samples were collected in three regions of Algarve at three different periods. Cluster analysis based on the propolis volatiles' chemical composition defined two main clusters, not related to the time of year, collection site, altitude, temperature or humidity ranges, and was based mainly on the relative amounts of viridiflorol, n-tricosane and n-nonadecane for cluster I. Cluster II was mainly characterised by the high thymol content, followed by viridiflorol, n-tricosane and n-nonadecane. The presence of higher thymol levels in propolis samples from cluster II may reflect the long use of an acaricide with thymol as main active ingredient. All samples showed an intense rock-rose aroma supported by the presence of characteristic Cistus and labdanum oil volatile components. Given the nowadays frequent propolis household use, volatiles thorough characterisation may assist in its quality assessment.