Not an easy question.... As far as I have been able to figure, standard (in as much as standards exist in this period) started to appear with greater frequency as the 17th century wore on. I haven't done any real reading on the English Civil War, but I had thought that the ECW was when uniformed soldiers first started to appear.... But I could be wrong on that, I know John Churchill First Duke of Marlborough was one of the biggest driving forces for standardizing the English Armies of the period, a lot of the conventions he put into place wound up defining warfare well through the 18th century.
I imagine it would be similar with the navy?