Johor Bahru is the state capital of the state of Johor and the second largest metropolitan area in Malaysia. Most tourists don't stop here and just pass through the city on their way to or out of Singapore. JB is a major local transportation hub however. Since it is just across the causeway from Singapore, some travellers use it as a hub to visit Singapore from here (lower accommodation prices) or to board the train, bus or airplane.
Kota Kinabalu is the capital of the state of Sabah on Borneo. With an estimated population of 532,129 in the city and 700,000 in the urban area, it is the largest urban centre in Sabah and the sixth largest in Malaysia. It is located close to Mount Kinabalu, the highest mountain in South-East Asia.