-Tropilaelaps koenigerum was first reported in Thailand. Species-diagnostic markers of bee mites, T. clareae and T. koenigerum were examined by sequencing of ITS and RAPD analysis. A lack of intraspecific polymorphism within T. clareae and T. koenigerum ITS was observed. At an interspecific level, 19 substitutions were found. Sequence divergence between ITS of these bee mites was 3.82%. A 5 bp (TTCTC) insertion was found in T. koenigerum. Based on ITS sequences, identification of these mites was simplified to restriction analysis of the amplified ITS with Mse I and/or Sau3A I. RAPD analysis using primers OPA07, OPA11 and OPA12 revealed 16 and 20 species-specific markers of T. clareae and T. koenigerum, respectively. A UPGMA phenogram based on genetic distance between pairs of geographic samples indicated clear differentiation between T. clareae and T. koenigerum genetically. Partial differentiation of T. clareae from different host species was observed.Tropilaelaps / bee parasite / RAPD / ITS / species-diagnostic marker / genetic diversity