In an attempt to know the elemental composition of two endemic Algerian thyme species, we analyzed eleven mineral and trace elements (Br, Ca, Cr, Cu, Fe, K, Mn, Rb, Sr, V, and Zn) in Thymus algeriensis Boiss & Reut. and Thymus capitatus (L.) Hoffm. & Link. These species are commonly used in Algeria as aromatic and medicinal shrubs. The total concentrations of chemical elements were determined by EDXRF spectrometry. The instrument calibration was assessed through the analysis of certified reference material CRM–336 (Lichen) from the IAEA, Vienna, Austria. The results show that the highest concentrations of the micronutrients (Br, Cr, Cu, Mn, Sr, V, and Zn) were registered in T. algeriensis, while the maximum concentrations of Ca, Fe, and the non-essential element, Rb, were found in T. capitatus. Potassium contents were similar in the two species. The concentrations of essential chemical elements in T. algeriensis leaves were found in the following order: K > Ca > Mn > Fe > Zn > Cu > Cr. However, the order of these elements in T. capitatus was Ca > K > Fe > Zn > Mn > Cu > Cr. Principal component analysis (PCA) showed that T. algeriensis was highly associated with Br, Cr, Cu, Mn, Sr, V, and Zn, while T. capitatus was correlated with Ca, Fe, K, and Rb. Dietary element intakes through ingestion of 1 teaspoon of dry powder (~ 10 g) were estimated and compared to recommended daily intakes and permissible limits under FAO/WHO guidelines. In all cases, these estimates were below those levels. These findings can enhance the dissemination of these medicinal plants, which have medicinal and organoleptic properties, and provide an experiment-based guidance to the pharmaceutical and food industries.