The chemical composition of stingless bee honey and propolis depends on the plant sources they are derived from, and thus reflects the flora available in the vicinity of the hives, the preference of the bee species, and the climate (altitude and temperature). To understand the relative influence of these factors, we studied the composition of honey and propolis. Samples from 24 colonies were analyzed: 12 from each of two Scaptotrigona mexicana meliponiaries located in the state of Chiapas in southern Mexico approximately 8.5 km apart. The chemical composition of honey and propolis was studied using NMR, and GC-MS, respectively. Antioxidant activity of propolis was also studied. Chemometric analyses were applied. The Tuxtla Chico honey samples contained higher concentrations of glucose and fructose, while the Cacahoatán samples displayed a rich composition of di- and trisaccharides. These differences can be attributed to the distinct nectar sources utilized by the bees in each location. Propolis composition in the two locations also demonstrated qualitative differences, indicating a specific choice of resins by the bees. The observed substantial variations in the chemical composition of propolis and honey of S. mexicana from two relatively close locations support the assumption that bee species cannot be regarded as the most important factor determining their chemistry.