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The objectives of this study were to investigate the prevalence and abundance of deer keds on various cervids in Lithuania, to molecularly characterize the deer ked species based on mitochondrial COI and 16S rRNA genes, and to compare them with Lipoptena species found in other countries. A total of 11,939 deer keds (Lipoptena cervi and Lipoptena fortisetosa) was collected from the fur of 30 cervids in Lithuania between 2015 and 2019. The values of infestation with deer keds differed among the species of the hosts. Moose and red deer were more frequently infested with L. cervi than with L. fortisetosa, while L. fortisetosa was found more often on roe deer. Phylogenetic analysis of the COI and 16S rRNA genes of five Lipoptena species revealed 110 and 55 variable nucleotide positions, respectively. Among Lithuanian samples, three COI haplotypes of L. cervi and three haplotypes of L. fortisetosa were detected, while there was no variation observed in the 16S rRNA sequences analyzed with one haplotype of L. cervi and one haplotype of L. fortisetosa. This is the first study on L. cervi and L. fortisetosa parasitizing cervids and the first molecular characterization of these deer ked species in Lithuania.