There are a few solutions I have used. Mechanics use markers in disassembly to ensure correct orientation when reassembling. Wax pencils and various "magic" markers will work. Of course black is not very evident, but silver is also available. I use the silver version occasionally.*
What I prefer is a paint marker, and specifically the fine line DecoColor brand by MARVY UCHIDA in the USA. They are made in Japan, and the brand name may be different for you. I have tried other, less expensive brands, and the tips seem to dry out quickly. I can leave a DecoColor marker for months, even a year or more capped, and it is still usable. Of course, it has the usual warning label as it contains xylene.
*Edit: Sharpie brand