Is there a way to do this? Only way I found in Google Chrome is by the bookmarks name, not domain.
You can use 2 extensions for that: "IO BookBar" and "SuperSorter".
First you use "IO Bookbar" to strip away all bookmark titles. Then you use "SuperSorter" to sort them. Since they don't have any title, they will be sorted by domain name.
Another solution is to prefix your bookmark titles manually, with the domain name or a short version of that.
and click on "Organize", there is a menu option called "Reorder by title"