There is described herein a method for specifically detecting Babesia species nucleic acid in a sample, which in one aspect comprises: (1) contacting a sample, said sample suspected of containing Babesia species nucleic acid, with at least two oligomers for amplifying a target region of a Babesia species target nucleic acid, wherein the at least two amplification oligomers comprise: (a) a first amplification oligomer comprising a first target-hybridizing sequence (i) that is from about 15 to about 33 contiguous nucleotides in length, is contained in the sequence of SEQ ID NO:66 and comprises SEQ ID NO:56 or 57; or (ii) that is from about 15 to about 33 contiguous nucleotides in length, is contained in the sequence of SEQ ID NO:96 and comprises SEQ ID NO:101; or (iii) that is from about 15 to about 33 contiguous nucleotides in length, is contained in the sequence of SEQ ID NO:97 and comprises SEQ ID NO:101; (iv) comprises or consists of SEQ ID NO:8; (v) comprises or consists of SEQ ID NO:83 and (b) a second amplification oligomer comprising a second target-hybridizing sequence that is from about 15 to about 33 contiguous nucleotides in length, and (i) is contained in SEQ ID NO:68 and comprises SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, or SEQ ID NO:85; or (ii) is contained in SEQ ID NO:67 and comprises SEQ ID NO:45 or SEQ ID NO:52; or (iii) is contained in SEQ ID NO:70 and comprises SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, or SEQ ID NO:51; (2) performing an in vitro nucleic acid amplification reaction, wherein any Babesia target nucleic acid present in said sample is used as a template for generating an amplification product; and (3) detecting the presence or absence of the amplification product, thereby indicating the presence or absence of Babesia species target nucleic acid in said sample.