Expression of several genes at the transcriptional, post-transcriptional, and epigenome level are modulated in order to design a better genotype through modifying the signalling pathways in response to different stress condition. In the recent times, the functions of a class of RNAs with little or no protein coding potential is an area of interest with the advancement and wide application of next generation sequencing technologies. Novel long non coding RNAs (lncRNAs) were discovered and advocated as one of the emerging players to understand important biological processes, growth and development besides stress response. LncRNA with length of more than 200 nt are reported to be involved in wide variety pf processes such as splicing, gene inactivation, and translation. Cucumber (Cucumis sativus L.) is one of the most important vegetable crops cultivated worldwide and serves as a model plant species for genetic and genomic studies because of rich source of genomic information. Ripening of the fruits, shelf-life and biological processes involved in post-harvest decay is poorly understood in a model non-climacteric crop like cucumber. RNA-seq analysis was conducted using a natural variant of cucumber (DC-48) with exceptional shelf-life with a contrasting genotype, DC-83 with very poor shelf-life. Suitable pipelines were used to develop a lncRNA database using these two contrasting genotype for better understanding of the post-harvest biology in cucumber.