The seasonal pollen index (SPI) is a continuing concern within the fields of aerobiology, ecology, botany, and epidemiology. The SPI of anemophilous trees, which varies substantially from year to year, reflects the flowering intensity. This intensity is regulated by two factors: weather conditions during flower formation and the inner resource for assimilation. A deterministic approach has to date been employed for predicting SPI, in which the forecast is made entirely by parameters. However, given the complexity of the masting mechanism (which has intrinsic stochastic properties), few attempts have been made to apply a stochastic model that considers the inter-annual SPI variation as a stochastic process. We propose a hidden Markov model that can integrate the stochastic process of mast flowering and the meteorological conditions influencing flower formation to predict the annual birch pollen concentration. In experiments conducted, the model was trained and validated by using data in Hokkaido, Japan covering 22 years. In the model, the hidden Markov sequence was assigned to represent the recurrence of mast years via a transition matrix, and the observation sequences were designated as meteorological conditions in the previous summer, which are governed by hidden states with emission distribution. The proposed model achieved accuracies of 83.3% in the training period and 75.0% in the test period. Thus, the proposed model can provide an alternative perspective toward the SPI forecast and probabilistic information of pollen levels as a useful reference for allergy stakeholders. Display omitted •A hidden Markov model (HMM) is proposed to predict seasonal pollen index (SPI).•Mast flowering stochasticity is combined with flower formation influencing factors.•Mast years' recurrence is parameterized via a transition matrix.•Relation between meteorological factors and SPI defines via emission distribution.•Probability of the next pollen level becomes available by using stochastic model.