Carotenoids exert multifaceted roles to plants and are critically important to humans. Phytoene synthase (PSY) is a major ratelimiting enzyme in the carotenoid biosynthetic pathway. PSY in plants is normally found as a small enzyme family with up to three members. However, knowledge of PSY isoforms in relation to their respective enzyme activities and amino acid residues that are important for PSY activity is limited. In this study, we focused on two tomato (Solanum lycopersicum) PSY isoforms, PSY1 and PSY2, and investigated their abilities to catalyze carotenogenesis via heterologous expression in transgenic Arabidopsis (Arabidopsis thaliana) and bacterial systems. We found that the fruit-specific PSY1 was less effective in promoting carotenoid biosynthesis than the green tissue-specific PSY2. Examination of the PSY proteins by site-directed mutagenesis analysis and three-dimensional structure modeling revealed two key amino acid residues responsible for this activity difference and identified a neighboring aromatic-aromatic combination in one of the PSY core structures as being crucial for high PSY activity. Remarkably, this neighboring aromatic-aromatic combination is evolutionarily conserved among land plant PSYs except PSY1 of tomato and potato (Solanum tuberosum). Strong transcription of tomato PSY1 likely evolved as compensation for its weak enzyme activity to allow for the massive carotenoid biosynthesis in ripe fruit. This study provides insights into the functional divergence of PSY isoforms and highlights the potential to rationally design PSY for the effective development of carotenoid-enriched crops. Carotenoids are a large class of lipophilic molecules that give flowers, fruits, and vegetables bright red, orange, and yellow color (Yuan et al., 2015b). In plants, carotenoids and their derivatives are critically important for plant survival and development (Nisar et al., 2015; Rodriguez-Concepcion et al., 2018; Wurtzel, 2019). Carotenoids are vital for photoprotection and contribute to light harvesting for photosynthesis (Niyogi and Truong, 2013; Hashimoto et al., 2016). They serve as precursors for biosynthesis of phytohormones abscisic acid and strigolactones (Nambara and Marion-Poll, 2005; Al-Babili and Bouwmeester, 2015) and are attractants to pollinators and seed-dispensing animals for plant reproduction. Carotenoid derivatives also act as signals for plant development and stress responses (Havaux, 2014; Hou et al., 2016) and provide aroma and flavors for fruits and vegetables. In addition, carotenoids provide precursors for vitamin A synthesis and are dietary antioxidants to lower the risks of some chronic diseases in humans (Fraser and Bramley, 2004; Rodriguez-Concepcion et al., 2018). Their essential roles in plants and health-promoting properties in humans have led to intense efforts to understand and manipulate carotenoids in plants (