Xylose/glucose isomerases are important industrial enzymes that are most widely used in food industries; however, their previously reported expression levels do not meet the requirements for industrial application. Here, an antibiotic resistance marker (ARM)-free system driven by ribosomal RNA (rRNA) promoters is developed to obtain high-level xylose/glucose isomerase (XI/GI) expression in Streptomyces rubiginosus (S. rubiginosus). The rRNA promoter rrnD yields the highest glucose isomerase production titer of XIs/GIs, which is eight times higher than that of ermEp* and 2.6 times higher than that of kasOp*. The integrated ARM gene is removed by further introduction of the Cre plasmid with a temperature-sensitive replicon. The production titer of XIs/GIs is further improved by replacing the xylR gene with an additional expression glucose isomerase cassette at the xylR locus. Ultimately, the glucose isomerase activity reaches up to 79.7 ± 7.5 U mL at 96 h. The results support the robustness and stability of XI/GI production with this ARM-free system using optimal ribosomal promoters in S. rubiginosus, demonstrating strong potential in large-scale industrial applications. Besides, the results imply that rRNA promoters are strong promoters that can be used for protein engineering or metabolic engineering.