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The Chilan Mountain cypress forest, northeastern Taiwan, is the only one where the genus Chamaecyparis is situated in a subtropical region. The health of a forest ecosystem is closely tied to the evapotranspiration (ET) of water through forests. This study focused on estimating the ET of old-growth cypress in the Chilan Mountain area and investigated its spatial variability in different watershed divisions using remote sensing. Our methods included applying hybrid image classification to generate land cover maps using Landsat-5 images, calculating habitat characteristics of old-growth using the Surface Energy Balance Algorithm for Land (SEBAL), investigating spatial variability of ET in relation to environmental parameters, and examining the gap-snag effect on old-growth cypress ET. The results indicated that the study area was classified into three land cover types (i.e., old-growth, non-old growth, and others). Old-growth had lower values in net radiance, the normalized difference vegetation index (NDVI), and daily ET than did non-old-growth. Watershed divisions at various scales did cause the variation on old-growth ET characteristics according to the selected parameters and the number of parameters for predicting the value of ET. Finally, ET between gap-snag and non-gap-snag habitats was statistically different. A higher proportion in gap-snag composition would lead to a lower value in daily ET and the NDVI.