They supposed it had been a spirit - That is, by whom the storm had been raised.

But when they saw him walking on the sea,.... See Gill on Matthew 14:26;

they supposed it had been a spirit; a phantom, a spectre, an apparition, a nocturnal demon:

and cried out; as men affrighted at the sight, and fearing they should be hurt by it, or that it portended some evil to them; See Gill on Matthew 14:26.

But when they saw him walking upon the sea, they supposed it had been a spirit, and cried out:

49. But when they saw him walking upon the sea, they supposed it had been a spirit, and cried out-"for fear" (Mt 14:26). He would appear to them at first like a dark moving speck upon the waters; then as a human figure; but in the dark tempestuous sky, and not dreaming that it could be their Lord, they take it for a spirit. Compare Lu 24:37.

6:45-56 The church is often like a ship at sea, tossed with tempests, and not comforted: we may have Christ for us, yet wind and tide against us; but it is a comfort to Christ's disciples in a storm, that their Master is in the heavenly mount, interceding for them. And no difficulties can hinder Christ's appearance for his people, when the set time is come. He silenced their fears, by making himself known to them. Our fears are soon satisfied, if our mistakes are set right, especially our mistakes as to Christ. Let the disciples have their Master with them, and all is well. It is for want of rightly understanding Christ's former works, that we view his present works as if there never were the like before. If Christ's ministers now could cure people's bodily diseases, what multitudes would flock after them! It is sad to think how much more most care about their bodies than about their souls.