Gray leaf spot (GLS) is a major foliar disease of maize caused mainly by Cercospora zeae-maydis and Cercospora zeina. Although both species infect maize, the comparative transcriptional programs between isolates of different species during maize colonization remain largely unknown. We conducted time-course pathogen-focused RNA-seq of one Jilin isolate assigned to each species during colonization of maize B73 under a controlled inoculation system. RNA-seq reads were mapped to the public C. zeae-maydis SCOH1-5 and C. zeina CMW25467 v3 reference genomes for transcript quantification and putative functional annotation. The C. zeae-maydis isolate developed visible symptoms earlier and showed greater pathogen-derived transcript representation at 6 dpi. The C. zeae-maydis isolate expressed slightly more reference-annotated cell wall-degrading enzyme (CWDE)-associated loci than the C. zeina isolate, whereas the numbers of expressed candidate effector-associated loci were similar. The C. zeae-maydis isolate also showed earlier or stronger host-associated induction of several CWDE- and candidate effector-encoding genes. Both isolates showed post-inoculation induction of candidate transcripts related to lipid metabolism, protease-related functions, and cercosporin biosynthesis, while a subset differed between isolates in the timing or magnitude of expression. RT-qPCR broadly supported the temporal trends of selected candidates. Together, these results define shared and contrasting transcriptional programs of two isolates of different Cercospora species during maize colonization.