In the third kind of GEP recombination, entire genes are exchanged between two parent chromosomes, forming two daughter chromosomes containing genes from both parents. The exchanged genes are randomly chosen and occupy exactly 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 emphasizing that this operator is unable to create new genes: the individuals created by gene recombination are different arrangements of existing genes. Obviously, if gene recombination were used as the unique source of genetic variation, more complex problems could only be solved using very large initial populations in order to provide for the necessary diversity of genes. However, GEP evolvability is based not only in the shuffling of genes (achieved by gene recombination and gene transposition), but also in the constant creation of new genetic material which is carried out essentially by mutation, inversion and transposition (both IS and RIS transposition) and, to a lesser extent, by recombination (both one-point and two-point recombination).