Humans have influenced the epidemiological patterns of American cutaneous leishmaniasis by habitat disturbance, which has led to the emergence of new transmission foci. In these transmission areas, detecting natural infection of sand fly species with Leishmania parasites is of prime importance in epidemiological studies. In this study, we examined the species composition, spatial distribution, seasonality, and natural infection with Leishmania of the sand fly fauna in an emergent leishmaniasis focus located in Colombia. Sand flies were collected from September 2014 to June 2015 using CDC light traps located in indoor, peridomestic, and outdoor habitats within areas with confirmed clinical patients. In total, 13,488 sand flies of 12 species and seven genera were collected. Among these, Pintomyia townsendi (Ortiz) was the most abundant species comprising 76.3% of total flies collected. The sand fly richness and abundance were influenced by habitat and weather conditions. Outdoor areas harbored the greatest diversity of sand flies. Rainfall negatively affected abundance, whereas increased temperature showed a low positive effect. We detected Leishmania amazonensis parasites in Pi. townsendi for the first time.