If the same base pairs are use to code for all organisms why is there so much variation among organisms

The order of the codons differs between organisms.

Explanation:

The four nitrogenous bases, guanine, thymine, adenine, cytosine (and uracil in RNA) are present in all living beings, forming pairs that are able to define our genetic characteristics. Nitrogen bases can have 64 different combinations, so there are 64 different codons. Of these codons, 61 will encode the 20 different types of amino acids in existence. The order that these bases are and the order that each codon is within the DNA is the factor that determines why there is so much variability among living things.

not sure if this is what you'r looking for eubacteria and archaebacteria