Trypanosomatids (Kinetoplastida:Trypanosomatidae) protozoa are a diverse group of obligate parasites. The genera Trypanosoma and Leishmania are the most studied because of their medical importance. This work aims to evaluate the effects of anthropization processes on the composition of the phlebotomine sand fly fauna and the natural infection by Trypanosomatids, with emphasis on Leishmania. At all 3,186 sand flies were collected, distributed in 13 genera and 52 species, being Ny. umbratilis the most abundant species. There was no difference in the diversity between canopy and soil environments. The species abundance and richness were higher in the forest environment while species diversity and evenness were highest in the forest edge. The ITS1 region was used by PCR-RFLP to identify the fragment profiles of Leishmania species, followed by genetic sequencing. Here were analyzed 100 pools of female sand flies, being six positive for DNA parasite. PCR-RFLP fragment patterns similar to Endotrypanum sp. were observed in Nyssomyia anduzei, Psychodopygus amazonensis and Lutzomyia gomezi, and those fragments similar to Leishmania (Leishmania) amazonensis were observed in Bichromomyia flaviscutellata. ITS1 sequencing confirmed the presence of Leishmania sp. in Bi. flaviscutellata, and Leishmania (Viannia) naiffi in Ny. anduzei, Psychodopygus amazonensis, and Lu. gomezi. This is the first record of Lu. gomezi and Ps. amazonensis infection by L. naiffi in the State of Amazonas. These results show the trypanosomatid infection in sandflies from different landscapes in a rural settlement, and the finding of species infected with L.(V.) naiffi suggest that they can develop a role in the transmission cycle of leishmaniasis.