This investigation was conducted at Agriculture Research station, Sakha, Kafr El-sheikh, Egypt during 2019 and 2020 rice seasons to study genetic diversity, combining ability and photosynthetic parameters in rice. A line x tester model was used in this study where five rice varieties were crossed with three testers. Four primers were used to estimate the genetic diversity of the studied paternal lines and the values of major allele frequency ranged from 0.62 to 0.75 and averaging 0.69. Genetic diversity values ranged from 0.37 to 0.47 and averaging 0.42.  The PIC values ranged from 0.43 to 0.61 and averaging 0.52. The GD dendrogram classified the studied rice genotypes into two main clusters: The first cluster included Giza 178 and Sakha 108, while the second cluster included the other genotypes.  Genetic distance ranged from 0.147 to 0.886 and the highest genetic distance was observed between Giza 182 and Sakha 178. Highly significant differences were detected among genotypes and their partitions for all studied traits. The highest mean values were detected for the crosses Sakha 107 x Sakha 101 for earliness as well as Sakha 108 x Sakha 101 and Giza 182 x Giza 179 for grain yield plant^-1. The mean squares due to SCA were much higher than those of GCA for all studied traits, indicating that the studied traits were governed by non-additive gene action. The parent Sakha 107 expressed the highest significant and negative gca effects for days to 50% flowering. Parent Sakha 108 seemed to be the best general combiner for grain yield plant^-1. The most desirable SCA effects for days to 50% flowering were detected for the cross Sakha 108 x Sakha 101, while the cross Giza 182 x Giza 179 expressed the most desirable SCA effects for grain yield plant^-1. The most desirable mid-parent and better-parent heterosis values were detected for the cross Sakha 107 x Sakha 101 for days to 50% heading and the cross Sakha 108 x Sakha 101 for grain yield plant^-1. The cross Sakha 108 x Sakha 101 expressed the highest mean values of cuvette temperature, leaf diffusive, net assimilation rate and stomatal conductance, while the cross Sakha 107 x Giza 179 gave the best values for transpiration rate.