Louse flies (Diptera: Hippoboscidae) are vectors of several blood-borne pathogens of wild birds, such as parasites of the genera Trypanosoma and Haemoproteus. We captured birds during the dry (March–April) and rainy (June–July) seasons in 2013 and 2014 using mist nets at five sites with different land-use types (urban and suburban forests, cattle ranch, shade coffee plantation, and well-preserved montane cloud forest). We thoroughly examined plumage of each captured bird to search for dipteran macroectoparasites. We used PCR to screen for haemosporidian parasites that could infect bird hosts parasitized by hippoboscids. The birds Chlorospingus flavopectus (prevalence: 0.6%, n = 150), Basileuterus rufifrons (1.8%, n = 56), and Sayornis nigricans (50%, n = 2) are first-time host records for the louse fly Ornithoctona fusciventris (Diptera: Hippoboscidae). We found a positive infection by Plasmodium/Haemoproteus parasites in C. flavopectus. This fly family includes many species that are vectors of bird pathogens; this has important implications for wild and domestic animal health.