Epizootiological study of Anaplasma marginale in regions that contain various reservoir hosts, co-existence of rickettsia pathogens, and common vectors is a complicated task. To achieve diagnosis of this rickettsia in cattle and campeiro deer of Brazilian Pantanal, a comparison was made between a real time polymerase chain reaction (RT-PCR) with intercalating Sybr Green fluorochrome and primers based on msp5 gene of A. marginale; a conventional PCR (C-PCR); and parasitological examination using thin blood smear stained with Giemsa-MayGrunwald. Both PCRs showed good performance in the diagnosis of A. marginale in cattle, and were superior to the parasitological exam. The RT-PCR detected seven positive campeiro deer (16.3%). This rate was significantly higher compared to C-PCR, which identified one animal as positive (2.3%), and also compared to parasitological diagnosis, which did not find any positive animals. The dissociation temperature average of positive reactions in cattle (81.72 ºC ± 0.20) was identical to dissociation temperature found in the cervids (81.72 ºC ± 0.12), suggesting that both animal species were infected with A. marginale. We concluded that RT-PCR can be used for A. marginale diagnosis and in epizootiological studies of cattle and cervids; in spite of the small number of campeiro deer samples, the results indicated that this wildlife species has importance in the Anaplasma epizootiology in the Brazilian Pantanal.