The natural colour spectrum of honey can vary from light amber to even black. It is dependent on several different factors such as:

-Mineral and ash content (higher levels result in a darker honey)

-Pollen content

-Plant origin

-Geographical origin

-Temperature (higher temperatures have been linked to darker colour)

– Plant pigments such as flavonoids (which also have antioxidant properties). Darker honey is associated with a higher amount of pigments and also a higher antioxidant content.

-Crystallization is a process that occurs naturally in honey.  Two main sugars in honey, glucose and fructose , influence the crystallization  of honey depending on their ratio. Honey with a high glucose:fructose ratio will crystallize faster than honey with a lower glucose:fructose ratio. During crystallization,  honey becomes lighter and more opaque. 

-Processing and handling honey and length of time stored can also affect the colour, making it become darker.

Darker honeys have also been associated with having a high antibacterial activity.