Beekeepers in Colombia are using almost exclusively Africanized hybrids which are considered to be more resistant to diseases and climatic conditions than European-derived honey bee populations. There are no reports of losses of larval and adult bee populations in the country due to infectious diseases. However, there is no official diagnostic system to detect the presence of pathogenic bacteria for Apis mellifera, such as Melissococcus plutonius and Paenibacillus larvae causing European foulbrood and American foulbrood respectively. To assess their presence and prevalence in a large sample sets, representatives of beekeeping populations in the country, we conducted a study on 491 of 5400 registered hives located in three regions in Colombia, analyzing larvae samples with conventional and molecular real-time PCR and molecular taxonomy techniques. Out of the two bacteria targeted, only M. plutonius was detected in 7 of the 491(1.4%) larval samples in all three regions in this sampling campaign. There was no evidence of symptoms consistent with European or American foulbrood. Therefore we are updating and confirming the low prevalence of M. plutonius and the no detection of P. larvae in an extensive sampling survey of Africanized bees at three different regions of Colombia. Our results are consistent with the view that africanized hybrid bees are more more resistant to diseases.