Tea clones and seed varieties released from Tocklai Tea Research Institutes are suitable primarily for manufacturing black tea (CTC/orthodox) while green tea manufactured from these clones are poor in quality. This led to identifying germplasm suitable for manufacturing green tea of high quality. Physiological parameters on net photosynthesis, transpiration, stomatal conductance, water-use efficiency, leaf temperature, and carboxylation efficiency of six selected germplasm (DH 1 and 2, DH 3 and 4, DH 5 and 6, DL 13, DL 25, and DL 39) were measured in first flush, second flush, rain flush, and autumn flush. Seasonal Yield, biochemical (L-theanine to total polyphenol ratio), and taster’s score were compared among seasons. Two protocols were used for green tea manufacturing, i.e., roasting and steaming. Significant differences in net photosynthesis (pn), stomatal conductance (gs), carboxylation efficiency (ci/ca), and yield were observed between flushes. Among the six test clones, the L-theanine to total polyphenol ratio found was highest in DH 5 and 6 in the roasting method. Structural and cluster analysis revealed that the DH clones genotypically occupied the same position as that of the popular green tea clone Longjing 43 of China and Yabukita of Japan, indicating suitability of these germplasm to develop new green tea clones. Clones DH 5 and 6 are suitable for green tea manufacturing and they can be released to the industry as new green tea clones. As far as manufacturing protocol is concerned, the roasting method of tea manufacturing was found superior over steaming.