Toll-like receptors (TLRs) are the earliest reported pathogen recognition receptors (PRRs), and these receptors play pivotal roles in the innate immune system. Systematic studies of TLR family at the genome-wide level are important to understand its functions but are currently lacking in the insect lineage. Here, 6 TLR genes were identified and characterized in housefly (Musca domestica). The TLR genes of housefly were classified into five families according to the phylogenetic analysis of insect TLRs. The domain organization analyses indicated that the TLRs were composed by three major components: a leucine-rich repeat (LRR) domain, a transmembrane region (TM) and a Toll/interleukin-1 receptor (TIR) domain. Primary and tertiary structure analysis showed that the ectodomains of arthropod TLRs were longer than that of other phyla or classes. The mRNA expression levels of all 6 TLRs downregulated in the resistant housefly strain. Moreover, the expression levels of 6 TLRs varied between tissue and gender. Additionally, the 3D structures of the TIR domain were highly conserved during evolution. Collectively, these results help elucidate the crucial roles of TLRs in the immune response of housefly and provide a foundation for further understanding of innate immunity of the housefly.