Chipotle chili peppers are dried and smoked jalapeño peppers. The Mexican import plays a big part in the Southwestern cusine.
 
 
Gourmet Sleuth
Chipotles chilies  [chee-POT-tleh] peppers are smoked jalapeno chili peppers and are also known as chili ahumado.  These chilies are usually a dull tan to coffee color and measure approximately 2 to 4 inches in length and about an inch wide.  As much as one fifth of the Mexican jalapeno crop is processed into chipotles. 

History
Chipotles date back to region that is now northern Mexico City,  prior to the Aztec civilization.  It is conjectured that the Aztecs smoked the chilies because the thick, fleshy,  jalapeno was difficult to dry and prone to rot.  The Aztecs used the same “smoke drying” process for the chilies as they used for drying meats.  This smoking allowed the chilies to be stored for a substantial period of time.

Today Chipotles are used widely throughout Mexico as well as in the United States.  Quite popular in the South Western U.S. and California;  Chipotles have found their way into the cuisine of many celebrity chefs from Hawaii to Manhattan.
   
(Oxford English Dictionary)
chipotle, n.
Cookery.
[< Mexican Spanish chipotle (1976 or earlier; 1953 or earlier as chilpocle; also as chilpotle) < Nahuatl

chil- (in chilli CHILLI n.) + poctli smoke.] 
A dried and smoked ripe jalapeño pepper, which is dark reddish-brown with a strong, piquant flavour, and is used esp. in Mexican cooking.
1950 C. P. LEAHY Spanish-Mexican Cookbk. (rev. ed.) 83 Chipotle, a popular golden brown chili, used sun-dried. 1952 M. RYWELL Mexican Cook Bk. 6 Chiles are the fruit of solanaceas [sic] plants and vary from region to region. Most commonly used are the Ancho, Chipotle, Cuararemo, Guero, Jalapeno, Mulato..and Serrano. 1967 E. L. ORTIZ Compl. Bk. Mexican Cooking 18 Chipotle, smaller than mulato and almost brick red, is available pickled as well as fresh.
 
18 October 1907, The Mexican Herald (Mexico City), pg. 10, col. 4:
Mexico City Produce.
(...)
Chile ancho, first, 11 1/2 kilos…8.75
Chile ancho, second, 11 1/2 kilos…7.00
Chile pasilla, first, 11 1/2 kilos…7.00
Chile mulato, first, 11 1/2 kilos…6.50
Chile mirasol, first, 11 1/2 kilos…4.25
Chile chipotle, first, 11 1/2 kilos…6.00…
 
12 December 1950, New York Times, pg. 14:
BLOOMINGDALE’S DELICACIES SHOP, 59th Street near Lexington Ave.
From Mexico:
Gay basket holds a whole tinned pineapple, strawberries, hot chile sauce, wild flower honey, liquid mole sauce, toasted chipotle chile in Daube sauce 7.50
   
15 April 1960, San Mateo (CA) Times, pg 6 ad:
HORKY’S MEXICAN RESTAURANTS
PANCHO’S PASTEL
A palate pleasing combination of Delicious Ham, Tender Chicken Morsels, Guacamole, Sour Cream and mild flavorful Chile Chiptole, from Mexico. Served with Arroz, Tender Frijoles, Tortillas and Butter…$2.25.