<p>The identification of the geographic origin of emeralds constitutes a crucial technique in gemological laboratories and holds a prominent position as a research focus within the gemology field. The proximity of the emerald deposits in Panjshir Valley, Afghanistan, and Swat Valley, Pakistan (just 250&#xa0;km apart) and their shared formation age of 23&#xa0;Ma pose significant challenges in distinguishing the origins of the emeralds from these two locations. Furthermore, the mineralization patterns of the emeralds from these two sites are not yet fully understood. The inclusion, spectroscopy characteristics and chemical composition of emeralds from these two deposits were systematically analyzed in this study through basic gemological tests, spectroscopic tests (infrared, UV-VIS-NIR and Raman spectroscopy), and major and trace element tests (LA-ICP-MS). There are a greater variety of inclusions in Pakistani emeralds, and that pyrite stands out as the most common inclusion found in emeralds from both sources. The patterns and frequencies of infrared and UV-VIS-NIR spectra of emeralds from the two deposits exhibit considerable promise for identifying their origins. As for the genesis of the two deposits, the low Li, Rb, and Cs contents of emeralds from both localities suggest that the ore-forming fluid was of metamorphic origin. The high Sc content of both is related to albitization of host rocks (Panjshir Valley) and deep hidden leucogranite (Swat Valley). This study provides an appropriate case for the origin identification by spectroscopic characteristics, proposes the element content standard for testing the source of ore-forming fluid, and verifies the geological characteristics of the two deposits through the element content.</p>