We aimed to investigate the molecular evidences on the role of ticks as vectors of Anaplasma and spotted fever group (SFG) Rickettsia species in southeastern Iran. A total of 815 tick samples were collected from different geographical regions of southern Kerman province. A 524-bp fragment of 16S rRNA and a 464-bp fragment of major surface protein 4 (msp4) of Anaplasma, a 962-bp fragment of outer membrane protein A (ompA) of rickettsiae, as well as an amplicon (ca. 800-bp) of internal transcribed spacer 2 (ITS2) of ticks were amplified by PCR technique. Ten nucleotide sequences, including three ompA, three ITS2, four Anaplasma (16S rRNA and msp4) were analyzed with BLASTn and phylogenetic software. According to ITS2 nucleotide sequences three tick species Hyalomma asiaticum, H. rufipes and Rhipicephalus sanguineus complex were identified. Rickettsia aeschlimannii was detected from Rh. sanguineus complex and H. rufipes, as well as A. ovis and a SFG Rickettsia was found in Rh. sanguineus and H. asiaticum, respectively. The present study reemphasizes the potential role of Rh. sanguineus complex in the natural cycle of ovine anaplasmosis in southeastern Iran. Our results also confirmed the presence of R. aeschlimannii in Rh. sanguineus complex and H. rufipes ticks for the first time in Iran. These results suggest a possible role of these ticks in the transmission cycle of R. aeschlimannii in southeastern Iran.