This study aimed to assess the possible relationship between the presence of Israeli acute paralysis virus (IAPV) of honeybees and disease symptoms development at the colony level, to describe the IAPV load in field colonies and to illustrate phylogenetic relationships between IAPV isolates in Andalusia (Spain). Presence and load of IAPV was studied in 96 colonies from all provinces in Andalusia. Epidemiological surveys were performed in all the colonies to assess their sanitary status. IAPV was found in 13.5% of the sampled colonies, and no association was observed between the presence of IAPV and disease symptoms at the colony level. An average IAPV load was established in 4.9•105 genome equivalent copies per bee. Phylogenetic analysis revealed that Andalusian isolates belong to a different lineage to a previously described isolate found in Valencia (2010). The results of this study will help us understand the epidemiology and effect of IAPV on Spanish colonies.