Can two different strains of a single species have different genomic sizes? I am not asking about plasmid. Can they have different sizes of actual chromosome?
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Yes, and one could argue that the differences between two strains of the same species are entirely due to their collections of genes (and therefore different genome sizes).
Take the plant pathogen Pseudomonas syringae, for example. There are many different strains, categorized by the plant hosts they cause disease on. This host range is determined by different collections of virulence genes in their genomes. So although they are the same species, they can be remarkably different in their genomes. See this (open access) paper by Baltrus, et al for more information.
A point to remember... "species" is a manmade concept, and there can be different definitions. Some species can have less than 90% similarity at the genome level!
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$\begingroup$ This answer seems decent, but I'm curious what example you have for that last sentence. $\endgroup$– HarrisCommented Jan 11, 2017 at 19:28
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$\begingroup$ I guess there are two ways to look at it... at the genome level, or homology of orthologous proteins. To keep with the example above, we found that several P. syringae strains have less than 80% similarity of orthologs. The same figure shows that there are on average 26 SNPs per KB, which is only 2.6% differences at the genome level, but that also is across only the genome portions that are actually comparable, and the overall differences at the nucleotide level are much higher. $\endgroup$ Commented Jan 12, 2017 at 17:36