We sell both, so we don't have much reason to talk one down to prop the other up. Here's the honest difference.
Warmth
Alpaca fibre is hollow, which traps air and makes it warmer, ounce for ounce, than merino. If you run cold or you're after something for genuinely cold days, alpaca is usually the better call. Merino is still warm — it just doesn't have alpaca's insulating edge.
Breathability and everyday wear
Merino has the advantage here. It moves moisture away from the skin slightly more readily and tends to feel less dense against the foot over a long day in a warm shoe. That's part of why it's the more common choice for office wear or anything indoors.
Softness
Alpaca is typically softer to the touch, with less of the faint prickle some people notice with wool against bare skin. If you've written off wool socks before because of that, alpaca is worth trying again.
Durability
Close to even. Both hold up well over years of ordinary wear when properly cared for; neither is meaningfully more fragile than the other in normal use.
So which one
Cold feet, outdoor days, boots: alpaca. Everyday wear, warmer settings, trainers: merino. If you can't decide, that's a reasonable position — most of our regulars end up owning both and choosing on the day.
To compare like for like, start with the Alpaca Crew Socks and the Merino Everyday Crew Sock: same height, different fibre. For boots, it's the Alpaca Boot Socks against the Merino Boot Sock.