In the third kind of GEP recombination, gene recombination, entire genes are exchanged between two parent chromosomes, forming two daughter chromosomes containing genes form both mothers. The exchanged genes are randomly chosen and occupy the same position in the parent chromosomes. Consider the following parent chromosomes:

Suppose gene 2 was chosen to be exchanged. In this case the following offspring is formed:

Note that, with this kind of recombination, similar genes can be exchanged but, most of the times, the exchanged genes are very different and new material is introduced in the population.

It is worth noticing that this operator is unable to create new genes: the individuals created are different arrangements of existing genes. Understandingly, when gene recombination is used as the unique source of genetic variation, more complex problems can only be solved using very large initial populations in order to provide for the necessary diversity of genes. However, the creative power of GEP is based not only in the shuffling of genes or building blocks, but also in the constant creation of new genetic material.