Indigo dye has a distinctive blue color and is one of the oldest known dyestuffs. In order to identify new Isatis genotypes for indigo production, 14 Isatis taxa collected from native area were grown under field conditions in Kahramanmaras,, Turkey. The effects of taxa and harvest times on leaf, indigo and indican yield were analyzed and compared with culture species (Isatis tinctoria and Isatis indigotica) by using spectrophotometer and HPLC. High indigo yield (87.13 kg/ha) was obtained from Isatis constricta and I. tinctoria subsp. tomentolla (Mersin location) had high indican yield (12.25 mg/g) in fresh leaves. The present work identified high indigo yielding taxa that may be used for genetic improvement in order to re-introduce Isatis species in the agricultural systems of Mediterranean regions. Especially I. constricta can be evaluated in terms of higher indigo yield than the native and culture taxa. I. constricta is an endemic plant in endangered category. This situation reveals that the need for the conservation of the species. To the best of our knowledge, there is no previous study reported about indigo contents of the studied 11 Isatis spp. so far.