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This study used MALDI-TOF MS and molecular tools to identify tick species infesting camels from Tamanrasset in southern Algeria and to investigate their associated microorganisms. Ninety-one adult ticks were collected from nine camels and were morphologically identified as <i>Hyalomma</i> spp., <i>Hyalomma dromedarii</i>, <i>Hyalomma excavatum</i>, <i>Hyalomma impeltatum</i> and <i>Hyalomma anatolicum</i>. Next, the legs of all ticks were subjected to MALDI-TOF MS, and 88/91 specimens provided good-quality MS spectra. Our homemade MALDI-TOF MS arthropod spectra database was then updated with the new MS spectra of 14 specimens of molecularly confirmed species in this study. The spectra of the remaining tick specimens not included in the MS database were queried against the upgraded database. All 74 specimens were correctly identified by MALDI-TOF MS, with logarithmic score values ranging from 1.701 to 2.507, with median and mean values of 2.199 and 2.172 ± 0.169, respectively. One <i>H. impeltatum</i> and one <i>H. dromedarii</i> (2/91; 2.20%) tested positive by qPCR for <i>Coxiella burnetii</i>, the agent of Q fever. We also report the first detection of an <i>Anaplasma</i> sp. close to <i>A. platys</i> in <i>H. dromedarii</i> in Algeria and a potentially new <i>Ehrlichia</i> sp. in <i>H. impeltatum</i>.