Bacterial spheroplasts do not divide but they grow and enlarge with DNA replication in a broth containing an inhibitor of peptidoglycan synthesis and high salt concentration. The enlarged spheroplasts of Lelliottia amnigena, belonging to the family Enterobacteriaceae, formed vacuole-like structures, while those of the aerobic photosynthetic marine bacterium Erythrobacter litoralis did not form such structures. In addition, the enlarged spheroplasts of L. amnigena, which differ in the size of inner and outer membranes, were larger than those of E. litoralis. To elucidate the reason for these differences, we analyzed the transcriptome (RNA-seq) of spheroplasts at the beginning of growth and upon enlargement. After sequencing the RNAs expressed in normal and enlarged spheroplasts, we compared the gene expression levels of the 1100 orthologs in E. litoralis and L. amnigena. Among these, 347 and 213 genes were more than 2-fold upregulated in enlarged spheroplasts of E. litoralis and L. amnigena, respectively; 193 and 269 genes were less than 0.5-fold downregulated in those of E. litoralis and L. amnigena, respectively. Thirty six genes were upregulated in L. amnigena enlarged spheroplasts but were downregulated in E. litoralis enlarged spheroplasts, and may be related to vacuole-like structure generation. Fourteen of the 36 genes encoded a membrane protein. Our findings indicate that spheroplast enlargement varies between different organisms with respect to gene expression.