The populations of honeybees and bumblebees have been decreasing around the world in the recent decades. A variety of pathogens and parasites, including bacteria, fungi, protozoa, nematodes, mites and insects play significant role in honeybee and bumblebee colonies loss. Parasites of the genus Nosema (Microsporidia: Nosematidae) and the genera Crithidia and Lotmaria (Kinetoplastida: Trypanosomatidae) have a significant negative impact on honeybee and bumblebee colonies. Recent studies of nuclear DNA markers of these parasites allowed to describe new species and genetic variants. The aim of this study was to investigate the Microsporidia (Nosema spp.) and Trypanosomatidae (Crithidia spp. and Lotmaria passim) prevalence and genetic diversity in honeybee and bumblebee populations of Indian territories that haven't been studied before. In total 119 specimens of 4 honeybee and 5 bumblebee species were analyzed in this study. The prevalence of parasites in honeybee and bumblebee populations of the two Indian states (Jammu and Kashmir, Karnataka) were identified using PCR with primers specific for the ribosomal RNA genes cluster of Nosema, Crithidia and Lotmaria species. Co-infection by microsporidian and trypanosomatid parasites was detected in several honeybee and bumblebee specimens from Jammu and Kashmir state. Comparative analysis of ribosomal RNA genes sequences showed that honeybee samples from India studied were infected by N. bombi, N. ceranae and L. passim. Bumblebee populations were infected by Nosema D, Crithidia bombi and Crithidia expoeki. No honeybee's specimen with trypanosomatid infection was found in Karnataka state. For the first time N. bombi infection was detected in the honeybee population. The studies of distribution of microsporidia and trypanosomatid parasites among the honeybee and bumblebee populations all over the World were summarized and supplemented.