I am using polygon layers from various sources to create species distribution maps however some of the layers have different polygon coordinates to others, therefore I cannot use them together as layers. Is there a simple way to change the coordinates of the polygon? I am relatively new to DIVA gis so any help is much welcomed.
I have not tried it, but the DIVA-GIS manual, section 10.1 describes the Tools->Projection option. If you know the projections of each layer, then you should have no problem converting them.
Another option would be to use QGIS to fix the input data, and then use DIVA-GIS for the domain specific operations you need.