How fast did this appear and has it be growing or is it nearly the same size as it was when you first spotted it?
I ask because I´m not sure that this is any primary attack from any microorganism.
I suspect that this is a secondary effect from a mechanical damage or from slime damage caused by stung of a coral.
When a fish gets a mechanical damage and / or damage to the mucous layer, it will be open for secondary bacterial infections. The unspecific defence system responds by sending macrophages to the injured area in order to fight the attack. In many fish – these molecules do not engulf the attacker (as in mammals) – instead they release their radicals (often H2O2) in the wound in order to lyse the attacker. This will also give tissue damages. To control these tissue damages – the fish use melanin – a potent antioxidant. The result of this will give dark brown or black patches in the fish skin. Normally – they not disappear with age.
I´m not say – that this is what´s happen with your fish – but it could be one explanation to consider
Sincerely Lasse
It has happened over the past week, both clowns have the dark marks/spots but only the larger clown has it more significantly on its body. You have a very good point after reading your response. I thought clowns don’t get stung by corals. They are swimming fine and eating. One thing I have noticed is more aggression when other fish enter there area of the tank. The whites of there body are clean without any black marks. This makes me think it’s not black ick