Single-cell transcriptome analysis through next-generation sequencing (single-cell RNA-seq) has been used broadly to address important biological questions. It has proved to be very powerful, and many exciting new biological discoveries have been achieved in the last decade. Its application has greatly improved our understanding of diverse biological processes and the underlying molecular mechanisms, an understanding that would not have been achievable by conventional analysis based on bulk populations. However, so far, single-cell RNA-seq analysis has been used mostly for higher organisms. For microorganisms, single-cell RNA-seq has not been widely used, mainly because the stiff cell wall prevents effective lysis, much less starting RNA material is obtained, and the RNA lacks polyadenylated tails for universal priming of mRNA molecules. In general, the detection efficiency of current single-cell RNA-seq technologies is very low, and further development or improvement of these technologies is required for exploring the microbial world at single-cell resolution. Here, we briefly review recent developments in single-cell RNA-seq of microorganisms and discuss current challenges and future directions.