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Phyllobates aurotaenia adults reach a maximum snout-vent length of 32 mm in males and 35 mm in females. The skin is slightly granular on the dorsum and smooth on the ventrum and limbs. The first finger is longer than the second, with all finger discs being narrow to moderately expanded. Toes are webless. Both maxillary and premaxillary teeth are present. Testes are unpigmented (Silverstone 1976).
This species has a black ground color, with two thin golden, orange, or green dorsolateral stripes extending from the base of the thigh and meeting at the snout (Silverstone 1976; Myers et al. 1978). The dorsal surfaces of the limbs are covered in gold, orange, blue, or green dots, and the ventral surface is black with blue or green dots (Silverstone 1976). Dotting is relatively sparse on the venter and more concentrated on the limbs (Silverstone 1976). The stripes are green or light yellow, and the ventral dots are always blue on individuals from Serranía de Baudó (Silverstone 1976). On individuals from the upper San Juan drainage, the stripes are yellow, light or dark yellow-orange, or light brownish gold (Silverstone 1976). There is a second form; some individuals, from above the Playa de Oro on the upper Rio San Juan, are larger and have broader dorsolateral stripes that are sometimes blended together by an orangish dorsal suffusion into one yellow-orange or red-orange stripe (Silverstone 1976; Myers et al. 1978).
Phyllobates aurotaenia juveniles are black with golden dorsolateral stripes, like P. terribilis juveniles. However, young P. aurotaenia have blue or green ventral spotting, which is not present in P. terribilis (Myers et al. 1978).
There are two forms of Phyllobates aurotaenia, a narrow-striped, slightly smaller form, and a broad-striped, slightly larger form, which do not always occur in the same place (Silverstone 1976). In the western Atrato drainage, the broad-striped form is absent and the narrow-striped form occurs up to at least 500 m (Silverstone 1976). In the Playa de Oro, it is not clear whether the narrow-striped form occurs at lower elevation than the broad-striped form; the two forms may simply be separated by a deep ravine (Quebrada Bochoramá) and not by elevation (Silverstone 1976).
Myers et al. (1978) speculates that there may be a cline between P. aurotaenia and P. bicolor, or hybridization, in the upper San Juan drainage. The largest specimens, which have the broad, fused dorsal stripes, come from above Playa de Oro on the upper Rio San Juan; these individuals more closely resemble P. bicolor in both coloration and size (Silverstone 1976; Myers et al. 1978). Phyllobates bicolor has a uniformly colored orange (red-orange, orange, or yellow-orange) dorsum lacking stripes. Phyllobates bicolor is also slightly larger (38.2 mm average size) than the broad-striped form of P. aurotaenia (32.1 mm average size), which is in turn larger than the narrow-striped form (26.3 mm average size).