Multiple eyewitnesses described Napoleon's hair as being various shades of brown. The reason he is sometimes portrayed or described as having very dark or even black hair is that on occasion he applied a lot of pomade to his hair.

Doctor Jean-Nicolas Corvisart in 1802:

His very fine chestnut hair, which, until the time of the expedition to Egypt, he had worn long, cut square and covering his ears, was clipped short.

Dennis Davidov at Tilsit in 1807:

None of the portraits that I had seen bore the least resemblance to him. Believing them, I had supposed that Napoleon sported a rather large hooked nose, dark eyes and dark hair... The hair on his head was not black, but dark reddish-blond; his eyebrows and eyelashes were much darker than the colour of his hair, and his blue eyes, set off by the almost black lashes, gave him a most pleasing expression.

Captain Ross of HMS Northumberland that took Napoleon to exile in 1815:

He is very sallow, with light grey eyes, and rather thin, greasy-looking brown hair, and altogether a very nasty, priestlike-looking fellow.

Louis Antoine Fauvelet de Bourrienne at Napoleon's death bed:

The Emperor had intended his hair (which was of a chestnut colour) for presents to the different members of his family, and it was cut off and kept for this purpose.

Many locks still exist and are various shades of brown with some gray strands. Bit hard to say what his original color was since over time the locks would have undergone some changes in color. In addition people tend be lighter haired in youth and then the hair goes darker with age.