The recent alarming loss of honey bee colonies around the world is believed to be related to the presence of viruses. The aim of this study was to detect two major viral diseases, Apis mellifera Filamentous virus (AmFV) and Israeli Acute Paralysis Virus (IAPV) using Reverse Transcription - Polymerase Chain Reaction RT-PCR, in honey bees in Mexico. Adult and larvae honey bee samples were collected from asymptomatic colonies of six major beekeeping regions in the state of Chihuahua, Mexico. Both viruses were detected in both developmental stages of honey bees, IAPV at a higher prevalence (23.5%) as compared to AmFV, only in 0.9% of samples. However, this is the first report on AmFV infection in Mexican apiaries. Further studies are required to understand the AmFV and IAPV impact on colony loss in Mexico and to develop strategies for enhancing the control of viral diseases.