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We have estimated the number of sika deer, Cervus nippon, in Hokkaido, Japan, with the aim of developing a management program that will reduce the level of agricultural damage caused by these deer. A population index that is defined by the population divided by the population of 1993 is first estimated from the data obtained during a spotlight survey. A generalized linear mixed model (GLMM) with corner point constraints is used in this estimation. We then estimate the population from the index by evaluating the response of index to the known amount of harvest, including hunting. A stage-structured model is used in this harvest-based estimation. It is well-known that estimates of indices suffer from large observation errors when the probability of the observation fluctuates widely; therefore, we apply state-space modeling to the harvest-based estimation to remove the observation errors. We propose the …