AbstractEuropean eel is critically endangered in Europe. Among other stressors, pathogens are well‐known to harm eels' fitness. One hundred and eighty‐two eels were captured in three Eel Management Units in Andalucía (SE Spain) and analysed for Anguillicoloides crassus, Anguillid herpesvirus 1 (AngHV1), the rhabdovirus Eel Virus European X (EVEX) and the aquabirnavirus Eel Virus European (EVE). A. crassus adults and preadults were isolated and morphometrically identified, and the eel swimbladders were artificially digested to count A. crassus larvae. Also, eel tissues were examined by PCRs for the presence of viruses. EVEX and EVE were not detected in any of the eels. The estimated prevalence (95% confidence limits) was 71 (64–78)% for A. crassus and 35 (28–42)% for AngHV‐1, varying these prevalences significantly between and within EMUs. Moreover, A. crassus prevalence was highest in smaller eels, in sites closest to the sea and eels sampled in the autumn. By contrast, AngHV‐1 prevalence was highest in biggest eels, in sites far from the sea and sampled in the summer or winter. However, in mixed effects logistic models including site as a random variable, the risk of infection was associated with distance to the sea in both A. crassus and AngHV‐1 infections and also to winter sampling in the case of AngHV‐1 and not to other variables. These results are evidence that both pathogens are highly endemic in eels from Andalusian habitats. Further studies are needed to better understand the risk factors associated with these pathogens on eel populations.