The color of honey has special relevance in the international market, as different markets demand specific colors of honey. Chile has very diverse native and exotic flora, which are used by bees (Apis mellifera) to produce a range of honey types, including honeys of different colors. In this context, determining the relationships between color and botanical origin among Chilean honeys is very relevant. The objectives of the present study were to compare three methodologies for determining color in Chilean honeys (Pantone®, optical density (OD), and Pfund) and to define the relationship between color and botanical origin of the characterized honeys. The most common honeys from the Libertador Bernardo O'Higgins Region (VI Region) of Chile were Galega officinalis, Quillaja saponaria, and Retanilla trinervia unifloral honeys, all of which have lighter colors than internationally described. Both the OD and Pfund methods could identify significant differences between dominant species; specifically, these methods were able to discriminate between G. officinalis and Q. saponaria honeys and between G. officinalis and R. trinervia honeys. The OD and Pfund methods revealed that honeys of G. officinalis (A530 nm: 0.93 and 95.53 mm Pfund) were darker than those of Q. saponaria (A530 nm: 0.42 and 80.66 mm Pfund) and R. trinervia (A530 nm: 0.35 and 73.41 mm Pfund). Although the three methods for determining the color of Chilean honeys had different efficacies, the OD method was able to discriminate among dominant species and honey types. Significant correlations among the dominant species were found for Chilean honeys from the Libertador Bernardo O'Higgins Region using both the OD and Pfund methods.