Two new species belonging to the Indo-Pacific gobiid genus Amblygobius are described from mud-bottom habitats. Amblygobius calvatus n. sp. is described on the basis of 9 specimens, 23.7–48.0 mm SL, from the El Nido area of northern Palawan in the Philippines. Diagnostic features for the new species include usual counts of 15 segmented dorsal and anal-fin rays, scales entirely cycloid, no scales on the head (including the side of the nape and upper opercle), 80–86 longitudinal body scales, 24–26 transverse body scales, a strongly lanceolate caudal fin, a grayish-brown color in life with two orange-brown stripes on the head and body, 8–11 small black spots or saddles on the upper back, a blackish moustache-like marking above the upper lip, a horizontally oval orange-brown spot on the opercle, and a white pectoral-fin base with a central, horizontally-elongate, reddish-brown marking. Amblygobius cheraphilus n. sp. is described from 11 specimens, 14.6–32.9 mm SL, collected near the town of Alotau in Milne Bay Province of Papua New Guinea. It differs from congeners on the basis of a combination of features, including usual counts of 13 segmented dorsal and anal-fin rays, scales entirely cycloid, no scales on the head except for the side of the nape, 56–60 longitudinal scales, 14–18 transverse scales, a moderately lanceolate caudal fin, a grayish color in life with two reddish-brown stripes on the head and body with the lower stripe containing a prominent oval dark-brown spot on the opercle and ending in a dark-brown spot on the caudal-fin base, a series of small brown saddles on the back and predorsal region, and a faint ocellus on the upper caudal-fin rays.