This study aimed to clarify the taxonomic position of an actinomycete isolated from an HIV-positive male patient with pulmonary complications in Asir, southern region of Saudi Arabia. The strain was found to have phenotypic properties typical of nocardiae and 16S rRNA gene analysis clustered the isolate with Nocardia wallacei (accession KC677696) in the phylogenetic branch of the amikacin resistance Nocardia transvalensis complex. We consider that nocardiosis is usually missed or misdiagnosed clinically and recognition of these bacteria based on phenotypic tests is strenuous, but definitive identification is attainable by molecular methods.