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Winter oilseed rape (Brassica napus) is one of the most cultivated oilseeds in the Czech Republic and belongs among major pollen allergens. Pollen allergies have an extensive clinical impact worldwide, and as well as in the Czech Republic. In this paper, meteorological variables such as mean air temperature, maximum and minimum air temperature, precipitation total and number of rainy days in the period 1991–2012 were studied using the PhenoClim phenological model to find the best predictor of the beginning of flowering of the Brassica napus in the Czech Republic. In addition, temporal and spatial evaluations of the beginning of flowering of the Brassica napus were examined at individual stations in different climatic zones within the same period. In total, three phenological stations at altitudes from 270 m asl to 533 m asl located in warm (W2), medium warm (MW7) or cold (C7) climatic zones were used for detailed evaluation. Based on the observation results at selected stations, the beginning of flowering of the Brassica napus advanced progressively in timing (nearly −15 days) in the 1991–2012 period. The base temperature and temperature sums were calculated for the beginning of flowering of the winter oilseed rape using the PhenoClim computer tool. As the most accurate predictor for the beginning of flowering of the Brassica napus, the mean air temperature was determined. The optimal start day for calculation was 30th January, the threshold (base temperature) was 6.0 °C and the temperature sum was 157.0 °C. The RMSE value was 4.77 and the MBE value was −3.00. The simulated data had a good correlation with the real observed data (the correlation coefficients were within the range from 0.56 to 0.76), and the PhenoClim model results indicate using them in the forecast modeling of the beginning of flowering of the Brassica napus in the Czech Republic.