Both Bikaner nd Jodhpur are Heritage Cities of Rajasthan. You should cover both Cities. In Bikaner You can visit Junagadh fort, Camel Research Center, Karni Mata temple, Gajner Palace. In Jodhpur You can visit Mehrangarh fort Jaswant Thada Umaid Bhawan Mandore
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Bikaner is 300km away from capital city which has history from 15th century. With hot climate prevailing September month is one such ideal time to visit. Junagarh fort, Laxmi niwas palace, kote gate, thar desert are some places to explore. Jodhpur is the metro city of Rajasthan ruled by Marwar dynasty which holds famous for ancient forts. With hot climate till September mid, it is a must place to visit. Mehrangarh fort, Umaid Bhavan palace, Phool mahal, museum and mahamandir temple are places to visit. My choice would be Jodhpur for it has more to explore and you need minimum of 3 full days. Since the distance between Bikaner and Jodhpur is 5 hours apart, when you plan kindly plan visiting both places.