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.