We present high-resolution (R ~ 50, 000) observations of near-IR transitions of CO and CN of the five known hydrogen-deficient carbon (HdC) stars and four R Coronae Borealis (RCB) stars. We perform an abundance analysis of these stars by using spectrum synthesis and state-of-the-art MARCS model atmospheres for cool hydrogen-deficient stars. Our analysis confirms reports by Clayton and colleagues that those HdC stars exhibiting CO lines in their spectrum and the cool RCB star S Aps are strongly enriched in 18O (with 16O/18O ratios ranging from 0.3 to 16). Nitrogen and carbon are in the form of 14N and 12C, respectively. Elemental abundances for CNO are obtained from C I, C2, CN, and CO lines. Difficulties in deriving the carbon abundance are discussed. Abundances of Na from Na I lines and S from S I lines are obtained. Elemental and isotopic CNO abundances suggest that HdC and RCB stars may be related objects, and that they probably formed from a merger of an He white dwarf with a C-O white dwarf.