Zebra Finches (Taeniopygia guttata) are distributed over most of Australia and have also been domesticated. Domestication in general has strong effects on various traits including reproduction. For successful reproduction choosing a suitable nest-site is essential. We focussed on two factors that might influence nest-site selection; height and cover. In two experiments, we investigated the nest-height and nest-cover preferences of five Zebra Finch populations (1 Australian, 4 domesticated). Our results revealed that all five populations preferred the highest nests and there were no differences between populations. With variation in nest-cover, the Australian birds and a less-selected domesticated population chose nests with cover, while birds from populations selected for specific plumage colourations used the open nest-boxes most. Nest-height preference seems to be conserved in domesticated birds, whereas preference for nest-cover seems to be modified during domestication. We discuss the intra-specific variation in nest-site preferences, in the light of evolutionary and domestication processes. We believe that this further understanding in nest-site preference can provide hints to understand the variation in breeding success of Zebra Finches across different experiments and laboratories.