By leveraging deep learning to automatically classify camera trap images, ecologists can monitor biodiversity conservation efforts and the effects of climate change on ecosystems more efficiently. Due to the imbalanced class-distribution of camera trap datasets, current models are biased towards the majority classes. As a result, they obtain good performance for a few majority classes but poor performance for many minority classes. We used two-phase training to increase the performance for these minority classes. We trained, next to a baseline model, four models that implemented a different versions of two-phase training on a subset of the highly imbalanced Snapshot Serengeti dataset. Our results suggest that two-phase training can improve performance for many minority classes, with limited loss in performance for the other classes. We find that two-phase training based on majority undersampling increases class-specific F1-scores up to 3.0%. We also find that two-phase training outperforms using only oversampling or undersampling by 6.1% in F1-score on average. Finally, we find that a combination of over- and undersampling leads to a better performance than using them individually.