There are often occasions where you want to use various different colors of thread on the same fly, whether as the thread in a dubbed body, ribbing, or for the head.
Tying in strands of various colors may add bulk in places where it is not appropriate. It can also add multiple bobbins to the array of gadgets hanging from the fly, and the smaller the fly, the more difficult this condition can become.
I have developed a method to overcome this problem. I use cream thread and then color it with waterproof markers as I tie. That way I can use an orange or red thread on the body with light colored dubbing for an interestingly realistic effect, and use a black marker (or dark brown) for the head or thorax. You can also make transitional color changes throughout the body of a dubbed fly by marking the thread and sparsely dubbing -- experiment.
It is necessary to allow enough time for the ink to dry, but that is much of a problem with waterproof pens. Lots of writers indicate they use colored head thread to indicate weighted nymphs, and this can be done easily with markers, too. coloring the thread before it is wound on is much easier than coloring afterwards, and allows greater control of what color goes where. Typical colors are black, brown, olive, orange, red, and yellow.
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