Diatoms are pivotal in global oxygen, carbon dioxide, and silica cycling, contributing significantly to photosynthesis and serving as fundamental components in aquatic ecosystems. Recent advancements in genomic sequencing have shed light on their evolutionary dynamics, revealing evolutionary complex genomes influenced by symbiotic relationships and horizontal gene transfer events. By analyzing 120 plastome and 70 mitogenome publicly available sequences, this paper aims to elucidate the evolutionary dynamics of diatoms across diverse lineages. In comparing genomic events between plastomes and mitogenomes, gene losses and pseudogenes were more frequently observed in plastomes, while they were less commonly found in mitogenomes. Overall, gene losses were abundant in the plastomes of Astrosyne radiata, Toxarium undulatum, and Proboscia sp. Frequently lost and pseudogenized genes were acpP, ilv, serC, tsf, tyrC, ycf42 and bas1. In mitogenomes, mttB, secY and tatA genes were lost repeatedly across several diatom taxa. Analysis of nucleotide substitution rates indicated that, in general, mitogenomes were evolving at a more rapid rate compared to plastomes. This is contrary to what was observed in synteny analyses where plastomes exhibited greater structural rearrangements compared to mitogenomes with the exception of the genera Coscinodiscus and one group of species within Thalassiosira.