The blacklegged tick, Ixodes scapularis Say, first reported in Indiana in 1987, has now been detected in more than half of Indiana’s counties. The first case of human granulocytic ehrlichiosis (human anaplasmosis) in Indiana was reported in 2002. We now report the detection of Anaplasma phagocytophilum and Babesia odocoilei (Emerson and Wright 1968) in I. scapularis ticks collected in northern Indiana. Using polymerase chain reaction analysis, 41 of 193 adult ticks (21.2%) collected from deer were positive for A. phagocytophylum, and 22 (11.4%) were positive for Babesia sp. Restriction fragment analysis of 12, and sequencing of another five of the amplified products identified these parasites as B. odocoilei. Five ticks (2.6%) were coinfected. Eight of 68 questing adult ticks (11.8%) were positive for A. phagocytophilum; seven (10.3%) were positive for Babesia sp. Six of the latter seven positive samples were determined to be B. odocoilei by restriction fragment analysis and sequencing of two samples. None of 39 pools of nymphs was positive for Babesia sp. Three of 15 ticks (20%) collected from a dog were positive for A. phagocytophilum and three ticks (20%) were positive for Babesia sp. One was confirmed as B. odocoilei. One tick was coinfected. This is the first report of the presence of these two agents in ticks in Indiana.