We report extensive chromosome homology revealed by chromosome painting between chicken (<i>Gallus gallus domesticus</i>, GGA, 2n = 78) macrochromosomes (representing 70% of the chicken genome) and the chromosomes of a turtle, the red-eared slider (<i>Trachemys scripta elegans</i>, TSC, 2n = 50), and the Nile crocodile (<i>Crocodylus niloticus</i>, CNI, 2n = 32). Our data show that GGA1–8 arms seem to be conserved in the arms of TSC chromosomes, GGA1–2 arms are separated and homologous to CNI1p, 3q, 4q and 5q. In addition to GGAZ homologues in our previous study, large-scale GGA autosome syntenies have been conserved in turtle and crocodile despite hundreds of millions of years divergence time. Based on phylogenetic hypotheses that crocodiles diverged after the divergence of birds and turtles, our results in CNI suggest that GGA1–2 and TSC1–2 represent the ancestral state and that chromosome fissions followed by fusions have been the mechanisms responsible for the reduction of chromosome number in crocodiles.