Using PCR in the direct diagnosis of bee virus infections has been shown to be an appropriate tool to overcome the difficulties of diagnosing bee virus infections. The occurrence of Israel acute paralysis virus (IAPV) and Kashmir bee virus (KBV) was investigated in honeybee colonies collected from ten different regions throughout Jordan by employing reverse transcription-PCR. The colonies were suffering from symptoms of depopulation, sudden collapse, paralysis, or dark coloring. The two viruses were identified in some of the collected samples: IAPV virus was present in 13% of samples, while KBV was present in 12%. The distribution of IAPV and KBV varied in the different geographic regions of investigation. The RT-PCR product for IAPV was 470–473 nucleotides, and for KBV was 408–409 nucleotides. Sequence analysis indicated that IAPV is most homologous to KBV.