Objectives: To characterise the genotypes of multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) isolated in Algeria, where there is a low MDR-MTB incidence rate. Methods: Ten MDR isolates and one resistant to isoniazid were investigated by PCR-Sanger sequencing for 10 loci involved in resistance. Amplicon-based next generation sequencing (NGS) of 15 loci was additionally performed on isolates harbouring novel mutations. Results: Sanger and amplicon-NGS provided the same results as with GenoType kits. Mutations known to be associated with resistance were described for most isolates: rpoB S531L in seven of 10 rifampicin-R MTB isolates, katG S315T in nine of 11 isoniazid-R, and promoter inhA c-15t in three of 11, embB M306V or M306I in two of two ethambutol-R, rpsL K43R in four of eight or rrs a514c associated with gidB L16R in streptomycin-R, gyrA A90V in the ofloxacin-R pre-XDR isolate. New and rare mutations were also described in rpoB (deletion 512-513-514), katG (S315R, M126I/ R496L), gidB (V124G, E92A, V139A, G37V), and gyrA (P8A). Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) profiles were similar for three isolates (lineage Cameroon), indicating a possible clonal diffusion in epidemiologically unrelated patients. Conclusions: Resistant MTB isolates in Algeria harbour resistance genotypes similar to other countries, but some rare patterns may result from selection and transmission processes inherent to the country.