Coxiella burnetii, the causative agent of Q fever, is a zoonotic pathogen for which epidemiological data are limited in Mongolia. This study investigated the presence of C. burnetii in ticks collected across Mongolia from forest, pasture, and livestock-associated environments. A total of 7,511 ticks were collected from 42 Soums across 12 provinces and 2 districts of Ulaanbaatar between May and June 2018. Molecular detection of Coxiella-related organisms was performed using 46 DNA samples, comprising 28 individual-tick samples and 18 pooled-tick samples representing 489 ticks, by nested PCR targeting IS1111 and the 16S rRNA gene. Twenty DNA samples (2 individual ticks and 18 pools) were PCR-positive. Sequencing and phylogenetic analysis revealed that 9 Hyalomma asiaticum tick pools contained 16S rRNA sequences of C. burnetii, whereas 11 Dermacentor nuttalli samples (2 individual ticks and 9 pools) contained 16S rRNA sequences of a Coxiellaceae bacterium. Two individual D. nuttalli ticks yielded IS1111 sequences closely related to C. burnetii, whereas the corresponding 16S rRNA sequences clustered with a Coxiellaceae bacterium, highlighting discordance between the 2 molecular targets. The C. burnetii sequences detected in H. asiaticum were closely related to clade A strains reported from the United States, Japan, Greenland, and Korea, whereas sequences detected in D. nuttalli clustered with Coxiella endosymbiont sequences. This study provides molecular evidence for the presence of C. burnetii in H. asiaticum tick pools in Mongolia and demonstrates that Mongolian ticks harbor genetically diverse Coxiella-related bacteria, highlighting the need for further investigation of their epidemiological significance.