The complex life cycle of Babesia bovis includes erythrocytic stages in the bovine host and other stages occurring inside its common tick vector Rhipicephalus microplus. In related apicomplexa, changing environmental conditions affect the expression of ribosomal RNA, but it remained unknown whether the polymorphic A, B, and C rRNA coding units of B. bovis are differentially expressed. Northern blot analysis confirmed that polymorphic regions in the B. bovis 18s and ITS-2 rRNA coding units are transcribed. Then, rRNA transcript expression profiles were compared by analyzing cDNA libraries generated from total RNA extracted from in vitro cultured parasites, B. bovis infected cattle, R. microplus larvae and egg sources. The 18s and ITS-2 expression profiles indicate that rRNA unit B is almost exclusively expressed in cultured parasites while units A, B, and C are co-transcribed in the in vivo total RNA sources. Collectively, the data indicate that differential transcription of rRNA occurs in B.bovis, depending on the life stage of the parasite and on the environment.