Mantua & Sabbioneta

Arc-et-Senans & Salins-les-Bains

Krumlov and Latran - where the castle is located- used to constitute two distinct towns separated by the river.

Regensburg and Stadtamhof: the latter was a rival neighbouring city until its incorporation in the 20th century.

With Cordoba: "Substantial political effectiveness was achieved by establishing these new cities within a short distance of the old centers that preceded them, following a Near Eastern tradition which was largely pre-Islamic. The examples of such twinned cities are multiple, on scales that are very diverse: besides the conurbation of Medina Azahara and Cordoba..." (AB ev)

Ubeda & Baeza

Buda and Pest, separate cities until 1873

La Chaux-de-Fonds & Le Locle

Dubrovnik and Ragusa were separate entities until the 12th Century.

With Medina Azahara

"the ancient twin towns of Maresha and Bet Guvrin" (AB ev)

Weimar & Dessau

Tilcara and Maimara are in such strong rivalry that it sometimes comes to physical violence between their inhabitants
See periodicolea.com

Santa Ana and Vale Colorado - Almost an entire page is dedicated to the description of their shared culture in the nomination file

Nice and Cimiez: Cemenelum (Cimiez) was an important rival of Nice, continuing to exist as a separate city till the time of the Lombard invasions. (Wiki)

Nan Madol and Lelu (The similarity between the two sites is stressed in the Nom file as well as the future intention to extend the nomination to include Lelu.)

Lednice & Valtice

Melaka and George Town rivalled over trade hegemony in the 18th / 19th century

Ano Vitsa and Kato Vitsa as well as Macro Papingo and Micro Papingo