A canine trail boot has a molded sole with raised lugs that divide the sole into individual pad cups that each receive a single pad from a dog foot. Independent movement between adjacent pad cups better replicates a dog's pad movement. The molded sole may include a toe having unidirectional treads, a tail having a combination of treads that also receive and retain straps, and a cushioning pad that protrudes into and engages with an indentation on a dog's paw to retain a boot securely. The sole interior may be layered with insoles that provide puncture resistance, heat isolation or reflection, and other custom interior features, or a liner may be provided that may also further incorporate the raised cushioning pad. The cushioning pad may be longitudinally adjustable within the boot interior, to tailor the cushioning pad to the ideal position to engage with a dog's metatarsal or metacarpal pad.