Question

why it is difficult to classify micro-organisms

Answer 1

It is difficult to classify bacteria because
(i) these are microscopic.i.e bacteria are too small to classify and it needs microscopes of higher resolution  to do that. 
(ii) there are limited differences in structure and function. 
(iii)  All bacteria have the same nucleic acid in there body, so they are very hard too classify because it was too small and look very same for that acid in their body. 
Hope this answer helped you.