Chromosome counts help in establishing relationships between species and between genera. And larger groupings too. Similarity in chromosome number may be evidence in favor of nearness in phylogeny, whereas difference in chromosome numbers may contradict presumed similarities.
For example, genus Oncidium. When we started doing chromosome counts, we discovered that there's more variation than there ought to be, giving evidence for the judgement that genus Oncidium is artificial, and may be formed by converging evolutionary adaptations within two or more disparate lineages.
Selective pressure may lead a variety of plants to undergo similar evolutionary adaptations, leading to the development of similarities among otherwise distantly related groups. This evolution of similar traits may obscure an underlying difference, leading to the conclusion that similar offshoots of disparate groups (A and B) are in fact a single group (group A-B), when they are in fact still quite different in underlying structure, even as they have developed apparent similarities. Chromosome count is a pretty good cue that something like this has happened, although it isn't decisive.
Does that explain it?