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The article presents a study that examines the association of the common bacterial types such as enterococci and Enterobacteriaceae in the avian nestlings of Pied Flycatchers Ficedula hypoleuca in central Spain. It explores the method of the study that obtains faecal samples from 54 broods on day seven and 13 after hatching to detect and estimate bacterial abundance. It outlines the result of the study, which indicates the correlation of Enterobacteriaceae loads with the mean temperature on day seven, however, they have negative link on day 13. Moreover, it indicates that Enterobacteriaceae are more sensitive to seasonal changes and climatic variation that enterococci.