Lutzomyia longipalpis, a sand fly, is a vector-spreading pathogenic protozoan in the New World. MicroRNA (miRNA) is evolutionarily-conserved non-coding RNA, which plays critical roles in various biological processes. To date, the functions of most proteins in L. longipalpis are unknown, and few studies have addressed the roles of miRNAs in this species. In the present study, we re-annotated the protein-coding genes and identified several miRNAs using a set of comparative genomics tools. A large number of L. longipalpis proteins were found to be homologous with those in the mosquito genome, indicating that they may have experienced similar selective pressures. Among these proteins, a set of 19 putative salivary proteins were identified, which could be used for studying the transmission of Leishmania. Twenty-one novel miRNAs were characterized, including two miRNAs, miR-4113-5p and miR-5101, which are unique to L. longipalpis. Many of the targets of these two genes were found to be involved in ATP hydrolysis-coupled proton transport, suggesting that they may have important roles in the physiology of energy production. Topology analysis of the miRNA-gene network indicated that miR-9388-5p and miR-3871-5p regulate several critical genes in response to disease development. In conclusion, our work provides a basis for improving the genome annotation of L. longipalpis, and opens a new door to understanding the molecular regulatory mechanisms in this species.