Functional DNA is best defined as DNA that is currently under purifying selection. In other words, it can't be deleted without affecting the fitness of the individual. This is the "maintenance function" definition and it differs from the "causal role" and "selected effect" definitions [The Function Wars Part IX: Stefan Linquist on Causal Role vs Selected Effect].
It has always been difficult to determine whether a given sequence is under purifying selection so sequence conservation is often used as a proxy. This is perfectly justifiable since the two criteria are strongly correlated. As a general rule, sequences that are currently being maintained by selection are ancient enough to show evidence of conservation. The only exceptions are de novo sequences and sequences that have recently become expendable and these are rare.
