Abstract The red-crowned crane in Japan was once
considered extinct due to hunting and habitat destruction in
late nineteenth century; however, in 1926, a small group of
cranes was rediscovered in the Kushiro Mire in eastern
Hokkaido. Since then, various conservation efforts,
including artificial feeding during winter, hunting prohi-
bition, and habitat conservation, have increased the popu-
lation size to [1400 by 2012. Despite such a successful
population recovery, the genetic characteristics of the
population have not been fully explored. To ensure the
long-term persistence and evolutionary potential of cranes,
accurate knowledge of the spatial distribution of genetic
variation and its underlying causes are necessary. We
assessed their genetic structure using 12 polymorphicmicrosatellite loci and inferred the mechanisms shaping the
observed structure. Among the three regional groups in
Hokkaido, we found generally low pairwise F ST values and
no significant differences in genetic diversity, probably
because of the population expansion in the recent past. In
contrast, spatial autocorrelation analysis revealed a signif-
icant positive kinship at the short distance (0–15 km) and
negative kinship at the long distance (155–205 km),
showing a pattern of isolation by distance. The presence of
isolation by distance on a small spatial scale despite the
species’ strong flight ability is probably explained by the
recolonization process and restricted dispersal due to natal
philopatry in a non-equilibrium condition. Cranes in
Hokkaido do not appear to be a panmictic (random mating)
population; however they can be considered a single pop-
ulation without genetic discontinuity (i.e. a single man-
agement unit). Our findings confirm the importance of
considering natal philopatry when developing management
strategies such as dispersing cranes into unoccupied areas.