Brown algae or brown seaweed is a commercial source of different polysaccharides/hydrocolloids including alginates and fucoidans. To increase the knowledge of transcript diversity and to understand the molecular pattern of alginate biosynthesis in brown seaweeds as influenced by tidal cycles, two RNA libraries were analyzed from Macrocystis pyrifera collected at the intertidal (0 m depth) and subtidal (10 m depth) zones. Yield and viscosity of sodium alginate were measured and scanning electron microscopy, as well as X-ray energy dispersion analysis of the sample materials were performed. Results revealed that frond samples from 10 m depth significantly produced more sodium alginate than that of 0 m depth. Corroborating the alginate yield data RNAseq analysis disclosed the overexpression of 8 alginate biosynthesis genes such as mannose-6-phosphate isomerase, phosphomannomutase, GDP-mannose 6-dehydrogenase, mannuronan C-5-epimerase, etc. at 10 m samples. Scanning electron microscopy study revealed the presence of alginate in the form of several trabecular structures in the meristematic cells of 10 m samples while the meristematic cells of 0 m samples were mostly found empty. To the best of our knowledge, this is the first transcriptome-based report of brown macroalga alginate production at different marine water depth.