The terms 'gene', 'organism', and 'species' have been used in a wide variety of ways in a wide variety of contexts. Genes are the entities which are passed on in reproduction and which control the ontogenetic development of the organism. Organisms are the complex systems which anatomists, physiologists, embryologists, histologists, and others analyze into their component parts. Species have been treated traditionally as the basic units of classification, the natural kinds of the living world, comparable to the physical elements. But these entities also function in the evolutionary process.
Genes provide the heritable variation required by the evolutionary process.
Traditionally, organisms have been viewed as the primary focus of selection, although considerable disagreement currently exists over the levels at which selection takes place. As one might gather from the title of Darwin's book, species are the things which are supposed to evolve. Whether the relatively large units recognized by taxonomists as species evolve or whether much less extensive units such as populations are the effective units of evolution is an open question.