© 2016 Veteriner Fakultesi Dergisi. All rights reserved.This study was conducted to determine the molecular prevalence and characterization of Haemonchus contortus from sheep along with the benzimidazole (BZ) resistance in H. contortus populations. Fecal samples were collected from a total of 300 sheep in research area and analyzed by fecal flotation. qPCR assays were utilized on trichostrongylid egg positive samples in order to identify H. contortus. Phylogenetic analyses were performed on ribosomal ITS-2 and mt-COI gene regions. BZ sensitive and resistant allele frequencies were determined by qPCR along with sequence analyses of the ß-tubulin isotype 1 gene for single nucleotide polimorphizms (SNPs). H. contortus was identified in 36 (24.8%) out of 145 trichostrongylid egg positive samples. H. contortus isolates showed 100.0% identity to each other and 0.1% difference with the isolates available in the GenBank based on phylogenetic analyses of ITS-2 gene while mt-COI analyses of the isolates exhibited a mean of 97.4±0.5% identity to each other and 5.5±0.8% difference with the isolates in GenBank. BZ sensitive and resistant allele frequencies in H. contortus populations were determined as 87.1%±16.2 and 12.9%±16.2, respectively. SNPs were detected only in the codon 200 of the sequenced isolates belong to resistant allele. This study provides the first data on molecular prevalence, phylogenetic characterization and BZ resistance in H. contortus populations from sheep in Turkey.