Individual marking techniques are critical for studying animals, especially in the wild. Current marking methods for bats (Order Chiroptera) have practical limitations and some can cause morbidity. We tested the p-Chip (p-Chip Corp.)—a miniaturized, laser light-activated microtransponder—as a prospective marking technique in a captive research colony of Big Brown Bats (Eptesicus fuscus). We assessed long-term readability and postimplantation effects of p-Chips injected subcutaneously above the second metacarpal (wing; n = 30) and the tibia (leg; n = 13 in both locations). Following implantation (Day 0), p-Chips were scanned with a hand-held ID reader (wand) on postimplantation days (PIDs) 1, 8, 15, 22, 32, 60, 74, 81, 88, 95, and over 1 year later (PID 464). For each trial, we recorded: (1) animal handling time; (2) scan time; (3) number of wand flashes; (4) p-Chip visibility; and (5) overall condition of the bat. Average scan times for p-Chips implanted in both the wing and leg increased over the duration of the study; however, the number of wand flashes decreased, suggesting that efficacy of p-Chip recording increased with user experience. Importantly, over 464 days both the visibility and readability of p-Chips in the wing remained high and superior to tags in the leg, establishing the second metacarpal as the preferred implantation site. Observed morbidity and mortality in captive bats with p-Chips was similar to baseline values for bats without these tags. Because scan efficiency on PID 464 was comparable with earlier days, this indicates that p-Chips implanted in the wing may be suitable as a long-term marking method. Our provisional results suggest that p-Chips are viable for extended field testing to see if they are suitable as an effective alternative to traditional methods to mark bats.