Hemoglobins play a key role in oxygen transport. High-oxygen-affinity hemoglobins are adaptive in hypoxic environments. To better understand adaptation to high-altitude hypoxia, we extracted RNA from the bone marrow of six Crested Ducks (Lophonetta specularioides) inhabiting the central high Andes of Peru (4,218–4,605 m elevation) and sequenced >2,000 expressed sequence tags (EST) from a non-normalized complementary-DNA (cDNA) library. Overall, we identified 1,692 ESTs in the expression profile representing 462 different genes. Among those, the ESTs that occurred at the highest frequency were the αA (major) hemoglobin subunit (HBA2; 22.7%), leukocyte cell-derived chemotaxin 2 (LECT2; 10%), αD (minor) hemoglobin subunit (HBA1; 9.6%), beta defensins (DEFB; 6.3%), and the βA hemoglobin subunit (HBB; 3.7%). These results provide the first quantitative identification of gene expression in bone marrow of individuals inhabiting high-altitude regions and are in agreement with the known hemopoietic and immune function of this tissue. The EST sequences identified here will be useful for a variety of studies focusing on other nontraditional model organisms. Further studies of Crested Ducks and other highland taxa will be required to determine whether the αA and αD hemoglobin subunits, which contribute to distinct isoforms with potentially different oxygen-binding properties, are differentially expressed in lowland and highland populations.