Simple SummarySand flies are insects that can transmit the parasites causing leishmaniasis, a major neglected tropical disease. In the Americas, these insects are highly diverse, and unlike what is observed for other vector-borne diseases, many species co-occur in sites where this disease affects human populations. Here, we present results from a two-year-long study where we study how the number of species changes in two rural areas of Western Panamá with different land use cover and through the dry and wet seasons. We found that species number increased during the wet season and in plots with higher natural forest cover and that species number decreased in both areas in plots when the forest cover decreased, with some species changing through the seasons, and some species disappearing when comparing the sand fly faunas of the most forested with less forested plots. However, our results suggest that seasonality, or the change from a dry to rainy season, can be a more important driver of the number of species locally observed in the studied areas.Cutaneous Leishmaniasis transmission in the New World is observed in areas with rich sand fly species’ faunas. The diversity and composition of sand fly species can change in response to seasonal weather and land use changes. Here, we present results from a two-year-long study where we collected, using Centers for Disease Control (CDC) light traps, sand flies from two rural areas, Las Pavas (LP) and Trinidad de las Minas (T) in western Panamá. Over 710 trap-nights, we collected 16,156 sand flies from 15 genera and 35 species. We identified 34 species in T, and the most abundant species collected was Nyssomyia trapidoi (Fairchild and Hertig, 1952) (n = 2278, 37%), followed by Psychodopygus panamensis (Shannon, 1926) (n = 1112, 18%), and Trichopygomyia triramula (Fairchild and Hertig, 1952) (n = 1063, 17%). In LP, we identified 26 species, and the most abundant species collected were Ty. triramula (n = 4729, 48%), and Ps. panamensis (n = 3444, 35%). We estimated a higher species’ richness in T (Chao2 ± S.E.: 36.58 ± 3.84) than in LP (27.49 ± 2.28). In T, species’ richness was significantly higher in the rainy season, but no seasonal differences were observed in LP. Species’ assemblages were nested in the two areas. Phlebotomine sand fly species’ abundance increased at the two sites during the rainy season. Our data suggest that seasonality is more important than land use as a factor driving sand fly species’ diversity at the studied sites.