Objective This study is to understand a comprehensive perspective on the molecular mechanisms underlying alternate bearing in mango (Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties. Results Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, alternate bearing etc. showed significant differences between these two different bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 alternate bearing genes were identified and principally three genes viz; SPL-like gene (GBVX01015803.1), Rumani GA-20-oxidase-like gene (GBVX01019650.1) and LOC103420644 (GBVX01016070.1) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene (gbGBVW01004309.1) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; alternate bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis. Conclusions Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with alternate bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the bearing tendencies in mango.