Provided herein are systems and methods for identification of gemstones. The gemstones can be identified without removing the gemstones from an object in which the gemstones can be set. The gemstones can be imaged and image analysis can quantify one or more external and/or internal characteristics of the gemstone. The quantification of the one or more external and/or internal characteristics of the gemstone can be compared to a previous characterization to positively identify the gemstone.