Background Keerom Regency remains one of the high-malaria-endemic regencies in Indonesia. Despite the accelerated malaria elimination strategy underway in Papua, malaria transmission in this regency has not declined. To characterize the entomological and human behavioral factors sustaining and driving malaria transmission, a rapid entomological assessment paired with human behavior observations (HBOs) and household surveys was conducted in five villages of Keerom Regency. Methods Entomological surveys were conducted on three occasions in 2022 and 2023. Human landing catches (HLC), night indoor resting collection, and mosquito larval site surveys were conducted alongside human behavior observations (HBO) and structured household surveys. Results Six species of Anopheles were identified including Anopheles koliensis , An. punctulatus , An. hinesorum , An. kochi , An. bancroftii and An. peditaeniatus . The dominant species were An. koliensis and An. punctulatus . Outdoor Anopheles human biting rates (HBR) averaged 1.4 ± 1.7 bites per person per hour (bph), higher than indoor HBRs of 0.8 ± 1.2 bph. Vector incrimination detected Plasmodium DNA in ten An. koliensis mosquitoes in 2023, including Plasmodium falciparum (n = 2, 20%), P. vivax (n = 7, 70%) and P. ovale (n = 1, 10%). Blood meal analysis showed mixed feeding on humans and dogs, with human blood indices of 58.3% for An. koliensis and 66.7% for An. punctulatus . HBOs highlighted a substantial gap in indoor protection during the early evening before sleeping. Household surveys identified several drivers of exposure, including the absence of window and door screens, limited indoor residual spraying coverage, low usage of insecticide-treated nets, and unprotected outdoor activity. Conclusions Members of the An. punctulatus group were abundant across all study villages, with An. koliensis and An. punctulatus being the primary species. Vector incrimination confirmed active malaria transmission. These vectors demonstrated opportunistic feeding behavior, primarily on humans but also on dogs, which may offer an avenue for targeted interventions. Multiple gaps in personal and household protection were identified, both indoors and outdoors. Strengthening indoor protection through increased ITN use, installation of house screens, and evaluation of complementary tools such as spatial repellents may reduce indoor transmission. Community-led larval source management in and around households may help reduce outdoor transmission.
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