The presence of phenolic compounds in honey can serve as potential authenticity markers for honey’s botanical or geographical origins. The composition and properties of honey can vary greatly depending on the floral and geographical origins. This study focuses on identifying the specific markers that can distinguish honey based on their geographical areas in the United States. The main approach presented in this study to identify the geographic origins of honey involves chemometric methods combined with phenolic compound fingerprinting. Sample clean-up and phenolic compound extraction was carried out using solid phase extraction (SPE). Reversed phase liquid chromatography in combination with tandem mass spectrometry were utilized for the separation of the compounds. The honey physicochemical qualities were predominantly determined via spectrophotometric methods. Multivariate statistical tools such as principal component analysis (PCA), analysis of variance (ANOVA), and partial-least squares discriminant analysis (PLS-DA) were employed as both classification and feature selection tools. Overall, the present study was able to identify the presence of 12 potential markers to differentiate the honey’s geographical origins. The total phenolic content ranged from 81.6 to 105.7 mg GAE/100 g corresponding to honey from Colorado and Washington, respectively (GAE: gallic acid equivalents). The regression analysis shows a tendency for the total phenolic content of honey to increase as the color of honey increases. The most important result obtained in this study is the demonstration that the geographical origin of honey plays a critical role in predicting the physical properties and phenolic composition of honey.