Rapid expansion of sika deer, in both number and distribution, in the Japanese Archipelago has resulted in serious ecological disturbance. In the present study, the population structure and migration patterns of sika deer (Cervus nippon) among Toyama and adjacent Prefectures were investigated using 11 polymorphic microsatellite loci. Deviation from Hardy–Weinberg equilibrium was detected in both total and individual regional sika deer samples from Toyama Prefecture. Results of pairwise F_ST results, factorial correspondence analysis, and STRUCTURE analysis indicated that sika deer in Toyama are not genetically distinct from those in adjacent Prefectures. Bayesian STRUCTURE results suggested the existence of two distinct clusters. However, multiple lines of genetic structure and high admixture were detected across the populations located in the central region of Toyama Prefecture. Both contemporary and historical migration analyses showed that dispersal into Toyama Prefecture from neighboring prefectures was high, especially migration from the prefecture on the east into Toyama Prefecture, and bidirectional dispersion between Toyama Prefecture and the prefecture to the south. Knowledge of such genetic structures and population dynamics is required for appropriate management and conservation of sika deer populations in the Japanese Archipelago.