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Chipotle vs Smoked paprika

The short answer

Two smoked capsicums, two different purposes. Chipotle is a ripe jalapeño smoked over wood and is genuinely hot as well as smoky. Pimentón de la Vera is a mild pepper dried over slow oak fires for a fortnight and carries the smoke with almost no heat. Both get their smoke from the same compounds — guaiacol and syringol — deposited on the flesh. The choice between them is a choice about heat, not about smoke.

Side by side

Chipotle and Smoked paprika compared side by side
 ChipotleSmoked paprika
Botanical identityCapsicum annuum L.Capsicum annuum L.
Part usedfruitfruit
OriginMexico, where smoking is the traditional answer to a chilli too thick-walled to sun-dry. The technique is documented well before European contact.The chilli is a New World plant brought to Spain in the sixteenth century; the smoking tradition is Spanish and is concentrated in the Vera valley in Extremadura, where the autumn is too damp for reliable sun-drying and drying over fire became the practical answer.
Flavour notessmoky, sweet, dried fruit, tobacco, moderately hotsmoky, sweet, resinous, earthy, faintly bitter
Heat2500–10000 SHU (typically 6000 SHU)0–5000 SHU (typically 500 SHU)
FlavourSmoky and sweet with a raisin-like depth, and a heat that arrives behind the smoke rather than in front of it. Meco is markedly smokier and less fruity than morita, which is the distinction worth knowing when buying.Sweet, smoky and slightly bitter, with a lingering resinous finish. The dulce grade has no heat at all; picante has a moderate warmth well below cayenne. Its sweetness comes from the sugars in the ripe flesh, which is also why it burns so readily.
AromaWood smoke over dried fruit — tobacco, raisin and a little chocolate. None of the green freshness of the fresh chilli survives.Wood smoke first, then sweet dried pepper underneath. The smoke is resinous and settled rather than sharp — it is a fortnight of slow oak rather than a flavouring — and this is the quickest way to tell a genuine product from a treated one.

Which should you buy?

Chipotle

Buy whole pods. Chipotle is one of the clearest cases for it: the smoke phenolics that define the spice are volatile and go first from the ground form, and a whole pod can be soaked and blended into a sauce in a way powder cannot. Ground chipotle is convenient for rubs and is a reasonable second jar, not a first one.

Smoked paprika

Full detail on chipotle and smoked paprika, including evidence grades and sources for every claim above.