Wi-Fi-based fingerprint indoor localization is widely used owing to its low cost and the rapid increase of its network, even though this method requires radio map creation and maintenance which accompany time-consuming and continuous monitoring. Considering these advantages and limitations and the fact that conditions in a ship are more likely to suffer from scattered and distorted wireless signals caused by a special structure of ship, this paper presents an efficient shipboard positioning technique using existing shipboard Wi-Fi network and additional ultra-wide band (UWB) nodes which are the IEEE 802.15.4a modules capable of precise positioning. The proposed method can reduce computational complexity that can occur during signal acquisition and automatically create and update more rapid and precise modified radio maps, by fusing the distance information obtained from UWB and Wi-Fi fingerprint. In addition, the advantages of proposed system are that selective computation technique which can remove weak signals is applied to reduce the amount of computation needed to create modified radio map and the positioning errors can be improved by assigning a positioning weight to each preceding position value because the same signal intensities can occur in other areas within the Wi-Fi network. The efficiency of the proposed method and its comparison with other methods are demonstrated.