Development of salt-tolerant genotypes is pivotal for the effective utilization of salinized land and to increase global crop productivity. Several cotton species comprise the most important source of textile fibers globally, and these are increasingly grown on marginal or increasingly saline agroecosystems. The allopolyploid cotton species also provide a model system for polyploid research, of relevance here because polyploidy was suggested to be associated with increased adaptation to stress. To evaluate genetic variation of salt tolerance among cotton species, 17 diverse accessions of allopolyploid (AD-genome) and diploid (A-, D-genome) Gossypium were evaluated for a total of 29 morphological and physiological traits associated with salt tolerance. For most morphological and physiological traits, cotton accessions showed highly variable responses to two weeks of exposure to moderate (50 mM NaCl) and high (100 mM NaCl) hydroponic salinity treatments. Results showed that the most salt tolerant species were the NE Brazilian allopolyploid G. mustelinum, the D-genome diploid G. klotzschianum from the Galapagos Islands, following by the African/Asian, A-genome diploids. Generally, A-genome accessions outperformed D-genome cottons under salinity conditions. Allopolyploid accessions did not show significant differences from either diploid genomic group in salt tolerance, but they were more similar to one of the two progenitor lineages. Our findings demonstrate that allopolyploidy per se need not be associated with increased salinity stress tolerance, and provide information relevant to utilization of the secondary Gossypium gene pool for breeding improved salt tolerance.