At the beginning of your upkeep, if you control a black permanent, you may put a +1/+1 counter on this creature.
At the beginning of your upkeep, if you control a green permanent, you may put a +1/+1 counter on this creature.
The “intervening ‘if’ clause” means that (1) the ability won’t trigger at all unless you control a permanent of the specified color, and (2) the ability will do nothing unless you control a permanent of the specified color at the time it resolves.
A permanent that’s both black and green will allow both abilities to trigger (as will separate black permanents and green permanents, of course).
