I have never wired with fish. There should not be many differences with other mitochondria. You could use mitosox, it seems the best available mitochondria probe. I do not know why you want to do it, but if you can fix the tissue you could look for classic markers such us carbonyls and nitrotyrosine. If you can isolate the mitochondria, again there is a number of tools you can use. With the information you provide, there is not much I can suggest right now.
I have frequently used Mitosox, the fluorescent dye reacted to the depolarization of electron transport chain in the inner mitochondrial membrane. The benefit of Mitosox is that its fluorescence remains once incubated at 37 degree for few minutes, even after you fix with formaldehyde and stain with some kind of antibody. I strongly recommend you to merge Mitosox and PGC1-alpha or PPAR-gamma antibody!!! PGC1-alpha is a master transcription factor for mitochondriogenesis, while PPAR-gamma promotes the lipid metabolism in mitochondria.
@Inan: No, MitoSOX permeates the cell membrane and targets mitochondria. In the presence of superoxide anions it is converted (i. e., oxidized) to a fluorescent product. Fluorescence microscopy allows you to detect this conversion.