Habitat suitability models can be generated using methods requiring information on species presence or species presence and absence. Knowledge of the predictive performance of such methods becomes a critical issue to establish their optimal scope of application for mapping current species distributions under different constraints. Here, we use breeding bird atlas data in Catalonia as a working example and attempt to analyse the relative performance of two methods: the Ecological Niche factor Analysis (ENFA) using presence data only and Generalised Linear Models (GLM) using presence/absence data. Models were run on a set of forest species with similar habitat requirements, but with varying occurrence rates (prevalence) and niche positions (marginality). Our results support the idea that GLM predictions are more accurate than those obtained with ENFA. This was particularly true when species were using available habitats proportionally to their suitability, making absence data reliable and useful to enhance model calibration. Species marginality in niche space was also correlated to predictive accuracy, i.e. species with less restricted ecological requirements were modelled less accurately than species with more restricted requirements. This pattern was irrespective of the method employed. Models for wide-ranging and tolerant species were more sensitive to absence data, suggesting that presence/absence methods may be particularly important for predicting distributions of this type of species. We conclude that modellers should consider that species ecological characteristics are critical in determining the accuracy of models and that it is difficult to predict generalist species distributions accurately and this is independent of the method used. Being based on distinct approaches regarding adjustment to data and data quality, habitat distribution modelling methods cover different application areas, making it difficult to identify one that should be universally applicable. Our results suggest however, that if absence data is available, methods using this information should be preferably used in most situations.