Abstract: Cyanobacteria are oxygen-evolving photosynthetic prokaryotes that synthesize organic substances from CO₂ and other inorganic nutrients. As a unicellular cyanobacterium, Synechococcus elongatus PCC 7942 can be cultured in large scale photobioreactors and easily genetically manipulated. Through systematic deletions of non-essential genes or regions, the genome of this cyanobacterium can be trimmed into a more suitable chassis for synthetic biological studies. The non-essential genes usually include those involved in responses to environmental changes or stresses. Even so, during the process of genome simplification, physiological effects of large fragment deletions should be monitored at each step. ∆Synpcc7942_0233-0253 and ∆Synpcc7942_2169-2187 are two mutants of S. elongatus with an 18 kb or a 14 kb deletion of non-essential genome region, named as Synpcc7942_0233-0253 and Synpcc7942_2169-2187, respectively. PCR examinations indicated that these mutants were completely segregated (no wild type genome copy was found). Comparisons of the two mutants and the wild type under different stressful conditions demonstrated that addition of 0.4 mol/L NaCl significantly inhibited the growth of the two mutants; under normal conditions, however, these 2 mutants showed no or very slight difference from the wild type.Under the salt stress condition, the photosynthetic activities of ∆Synpcc7942_0233-0253 and ∆Synpcc7942_2169-2187 decreased to 41% and 51% of wild type at 96h, respectively; in contrast, the two mutants showed increased respiratory activities. The salt stress reduced electron transfer reactions (ETR) of photosystems (PS) II in the wild type by 52%, in ∆Synpcc7942_0233-0253 by 77% and in ∆Synpcc7942_2169-2187 by 82%. At the same time, the ETR of PS I decreased by 32% in the wild type, by 50% and 47% in the two mutants, respectively. We reported two examples of large genomic fragment deletion mutants with greatly reduced stress tolerance, and the findings provided necessary information for the design of chassis genome of the cyanobacterium and the control of conditions for industrialization in the future.