Eumusae leaf spot disease, caused by Mycosphaerella eumusae, is widely distributed in different banana growing countries in Asia and Africa, causing severe losses in yield and quality of banana. The aim of this study was to identify the differentially expressed defense responsive genes through subtractive suppression hybridization (SSH) in the Musa-M. eumusae interaction system. In this method, leaf samples collected at different intervals between 0 and 72 h postinoculation (hpi) of M. eumusae from resistant (Manoranjitham-AAA) and susceptible (Grand Naine-AAA) cultivars were subjected to cDNA-SSH library construction. From the SSH library, 832 clones having the insert were selected and sequenced. All these sequences were assembled using CAP3, which resulted in 498 unigenes (59.85%), consisting of 78 contigs and 420 singletons. Furthermore, the BLAST2GO analysis performed showed that, out of the 498 unigenes, only 161 (32.32%) were involved in molecular functions, cellular component and biological processes. However, among these 161 unigenes, 57 were found to have top BLAST hits. Six genes were selected based on the function and subjected to validation through qPCR. Four genes, namely ethylene responsive factor, flavin containing monoxygenase, serine glyoxylate, and metallothionein, were found to have the highest-fold regulation in the resistant cultivar at 48 hpi, followed by lipoxygenase at 36 hpi. The main findings are that resistant plants deploy HR activity as a strategy to evade the fungus followed by the activation of various ROS scavengers to maintain homeostasis and the role of phytohormones may be induced as a part of plant defense against M. eumusae.