Avian malaria remains an obscure and mostly unknown avian infection despite the socio-economic threat it poses for poultry industries and its potential to hinder conservation efforts. Therefore, diagnostics for the infection should be expedient, efficient and flexible in applicability. We compared and contrasted two diagnostic techniques for avian malaria; microscopy and polymerase chain reaction (PCR).We also used both methods to determine the basic distribution and prevalence of avian malaria amongst passerines in the Western Cape. Approximately 1000 birds from 49 species were sampled from 26 wetlands across theWestern Cape and examined for avian malarial infections. Infections were categorized by genus of malarial pathogen and by bird species infected. Using ocular diagnosis, 183 (18%) birds were infected, compared to 221 (23%) birds diagnosed with PCR. Plasmodium spp. were found to be the predominant cause of infection using both techniques, followed by Haemoproteus and Leucocytozoon, respectively. Although outcomes from both techniques were strongly correlated, PCR was superior in terms of its sensitivity and expediency. PCR also has wider applicability for users with varying experience in malarial diagnostics, further endorsing molecular diagnostics as the default technique for in-depth analysis of avian malaria epidemiology.