diff --git a/kwant/builder.py b/kwant/builder.py
index f245a0fb57ee4faece7387e646992d00ad27719c..d5e4b1617311639c1fabbf7cc05786a8681f9e7e 100644
--- a/kwant/builder.py
+++ b/kwant/builder.py
@@ -1342,7 +1342,7 @@ class Builder:
             # site in FD of other.symmetry, so we must map it correctly
             hoppings = [(sym.to_fd(site), n) for n in other.neighbors(site)]
             for hopping in to_domain(domain, hoppings):
-                add_site(hopping[1])
+                add_site(self.symmetry.to_fd(hopping[1]))
                 try:
                     self[hopping] = other[hopping]
                 except KeyError: