Why different flowers have different colors?

We do not know in any clear way what originally produces the different colors in different flowers. Without implanting biotechnology and genetic engineering we can not alter the color of any particular flower to any great extent, even when we have the seed from the beginning, unless we blanch it by growing it in a soil that has no iron. The color of a particular flower is what it is through heredity – the general law that offspring resemble their parents.

This acts in a very remarkable way in some cases which are now being studied, especially in the color of sweet-peas, which vary a great deal as we all know. It may seem to us that these variations are just haphazard – white and pink and purple, and so on, occurring by chance in flowers of the same plant (see photo). But it is not so. The different colors occur in regular proportion, due to the way in which the laws of heredity work. And if we take seed from these flowers and grow it, we find that these laws are still maintained in the color of the flowers of the next generation. We know, too, that the single cell from which every plant starts contains the genetic program that determines what color of flowers it shall have, and what proportion of each kind of color is to be in these flowers.

Additional reading:
Flower (Wikipedia)
Sweet pea (Wikipedia)

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