If the eyes are the window to the soul, then of course Arthur and Merlin's were the same color. It only made sense, now that looked at them with this knowledge. The dragon had always said that Arthur and Merlin were two sides of the same coin, but this speculation was taking it a step further.
After the last magical incident that put Camelot in great peril, Gaius had had to do some reading. There seemed to be a being possessing innocent men and women to do their bidding. It was almost impossible to catch unless you looked directly into the person's eyes. Whenever someone was possessed their irises would bleed into their pupils, causing the black dots of normality to disappear, leaving the victim's eyes entirely one color, whether it be green, blue, brown, or the like.
So, naturally, in order to find the means of which Merlin was to bring about this creature's downfall, Gaius had to do some research on eyes and their magical properties.
Gaius had known eyes to be the weak spot of many possessive or controlling demons before, but, what he didn't know was the reason for this was because the eyes were the windows to the soul.
The fact had startled the old man, wondering what on earth it meant. It did explain, however, why someone possessed would have a change in eyes, their soul being twisted or manipulated in some way.
The creature was vanquished without incident (well, besides Merlin being possessed and nearly smiting everyone with his magic, leaving the final rescue up to the old man himself) and things settled back to normal.
But the words from those ancient texts still curiously toyed with Gaius mind and he made a better habit of keeping eye contact with anyone who made him wonder. And who made him wonder more than Merlin?
So, the next time the old physician saw the two destined lads side by side, he looked into their eyes and was left astonished by what he saw.
He'd always known that Merlin and Arthur had had the same color eyes, of course, but this was different. It were as if their eyes were identical, down to the way they moved, the way they gleamed, the way the colors swam within them . . . It was mind boggling. And when the two young men left him, utterly clueless about his discovery, Gaius gaped after them, his own eyes wide.
He'd known the two boys were close, closer than any two people he'd seen before. But now, as he saw what lied beneath, it could not be denied.
Merlin and Arthur shared the same soul and were destined to be by each other's side. It was no wonder they were so hard to break apart. Without the other, they weren't whole.