Peels of edible fruits from Hylocereus genus have been investigated as possible sources of pectins. In the present study, peels of H. undatus (red peel and white pulp) and H. costaricencis (red peel and red pulp) were extracted using the enzyme preparation Celluclast® (111 μL/g, pH 5, 50 °C for 1.5 h) and conventional acid extraction (boiling 0.1 M nitric acid for 60 min). The monosaccharide composition and the degree of methyl-esterification (DM) were determined by chromatographic and spectroscopic methods. It was possible to obtain pectins with GalA ≥65% from H. undatus and H. costaricencis peels by acid and enzymatic extractions with similar yields. Pectins obtained by acid extraction had higher DM (>50%) and GalA content. The enzymatic extraction resulted in pectins with DM < 50% and higher molar mass. High methoxyl pectins obtained by acid extraction were characterized by NMR analysis. Oscillatory rheological measurements showed they were able to form gel at concentration ≥1% (w/w), 60% sucrose at pH 2.5. Comparing the two species, the pectin obtained from H. undatus peels had longer side chains, higher DM and molar mass than the pectin from H. costaricencis peels. It was demonstrated for the first time that pectins with commercial features can be obtained from peels of H. undatus and H. costaricencis by acid extraction.