Dark chocolates were characterized according to geographical origin, cocoa variety, and cocoa content using the methylxanthine and polyphenolic composition and antioxidant activity as the data. The main study objective was to uncover sample patterns and identify possible markers of quality, variety, or origin to deal with authentication or fraud detection issues. In the study, a set of 26 dark chocolates from different varieties (e.g., Criollo, Forastero, and Trinitario) harvested in Africa, America, and Asia was analyzed. The optimized sample treatment consisted of defatting the chocolate (1 g of sample with 5 mL of cyclohexane for 15 min, three times) and then extracting the analytes by sonication with methanol/water 60:40 (v:v) for 15 min. The filtered extracts were analyzed by reversed-phase high-performance liquid chromatography with UV and spectrophotometric methods (Folin-Ciocalteu, ferric reducing antioxidant power, and aluminum methods) to determine individual phenolics and overall indexes of antioxidant and flavonoid content. Results from this chocolate set indicated that American samples are richer than African counterparts in alkaloids and phenolics (e.g., 1.7 vs. 1.1 mg g caffeine and 14.5 vs. 12.5 mg g total flavanols, respectively). Regarding cocoa varieties, Criollo cocoa was richer in bioactive compounds and antioxidant capacity (e.g., 16, 15, and 12 mg g total flavanols for Criollo, Forastero, and Trinitario, respectively). These results indicate that the analytes resulted in potential descriptors of varietal or geographical attributes.