Stomatal pores, representing around 1% of total leaf surface, are the main gates for plant gas exchange, thus playing an important role in photosynthesis and water relations. Under saline conditions, operation of stomata is severely affected by adverse effects of salt on biochemical and physiological processes in guard cells (GCs), reducing CO2 assimilation and causing yield loss. Next generation sequencing (NGS) technologies such as transcriptome and proteome analyses may be powerful tools in understanding the mechanistic basis of GC operation under saline conditions. As such studies require a large number of cells, developing an appropriate isolation method to provide adequate supply of GC with a sufficient purity is a critical step in this process. The most widely used method is isolation of GC protoplasts although it comes with some certain limitations. A viable and better alternative may be using GC-enriched epidermal. The modified protocol showed more efficacy and was more enriched in GC-specific genes suggesting the suitability of this approach for exploring responses of GCs to environmental and chemical stimuli at the molecular level. Application of GC-enriched epidermal fragments method for proteomics analysis proved to be efficient in understanding the mechanistic basis of stomata operation under saline conditions. Omics studies could be applied in conjunction with other research tools such as genome editing at GC level to identify new genes or proteins conferring stomata function which can then be targeted by breeding program to produce plants with better stomatal performance under adverse environmental conditions.