In the present study, we discovered a relationship between down-going and up-going route preferences and selection of spatial reference. The participants were asked to choose between a down-going route and an up-going route on a simplified map. When they were asked to select the better route (Experiment 1), they preferred the down-going route, although the two routes were the same shape and distance. However, when the participants were asked to select the route that seemed easier to remember and find, they favored up-going routes (Experiment 2). We suggested that the contrary route preferences were caused by different selections of spatial references. That is, the first instruction directed participants’ attention to the configurational layout of the maps (i.e., promoted the allocentric reference) and induced the down-going route preference, whereas the later instruction promoted egocentric navigating strategies and induced the up-going route preferences. Furthermore, we asked the participants to learn a down-going and an up-going route, then examined their wayfinding and spatial memory performance (Experiment 3). The participants found the goals more quickly when up-going routes were used, but remembered the locations of landmarks more accurately when down-going routes were used.