Create a character style that has the color you want, and apply it to the > symbol. There are two ways to do this automatically.
If the number of occurrences is predictable in a paragraph, an ordinary nested style in your paragraph style definition can be used, i.e. [None] up to 1 >, <your character color style> through 1 > and repeat the pattern as many times as required.
Better, and necessary if the number is not predictable, would be to use a GREP style and apply the style to the text > and it will change the color wherever it appears in paragraphs with that style.
And if you haven't applied a unique paragraph style to the list and there are going to be occurrences of > that you don't want in the other color, you can also apply the character style manually, or by using Find/Change on a selected list.
Thanks all, the GREP thing was exactly what I was looking for. Tried a google first but don't think I was wording my request correctly.