In two-point recombination the chromosomes are paired and the two points of recombination are randomly chosen. The material between the recombination points is afterwards exchanged between the two chromosomes, forming two new daughter chromosomes. Consider the following parent chromosomes:

0123456789001234567890    
+*a*bbcccac*baQ*acabab-[1]
*cbb+cccbcc++**bacbaab-[2]

Suppose bond 7 in gene 1 (between positions 6 and 7) and bond 3 in gene 2 (between positions 2 and 3) were chosen as the crossover points. Then, the paired chromosomes are cut at these bonds, and exchange the material between the crossover points, forming the offspring below:

0123456789001234567890    
+*a*bbccbcc++*Q*acabab-[3]
*cbb+ccccac*ba*bacbaab-[4]

Note that the first gene is, in both parents, split downstream from the termination point. Indeed, the noncoding regions of GEP chromosomes are ideal regions where chromosomes can be split to cross over without interfering with the ORFs. Note also that the second gene of chromosome 1 was also cut downstream from the termination point. However, gene 2 of chromosome 2 was split upstream from the termination point, profoundly changing the sub-ET. Note also that when these chromosomes recombined, the noncoding region of gene 2 of chromosome 1 was activated and integrated into chromosome 3.

The transforming power of two-point recombination is greater than one-point recombination, and is most useful to evolve solutions for more complex problems, especially when multigenic chromosomes composed of several genes are used.