The accurate identification of an organism is the basis of all biological disciplines. Although there have been many different species concepts and methods proposed, researchers generally choose the most appropriate concept according to their interests. However, each species concept has both advantages and disadvantages. In such cases, an integrated concept based on evidence obtained from different species concepts and methods is suitable for the accurate delimitation of a species. The biggest dilemma of integrated species delimitation methods is the inconsistency between species concepts and methods. Herein, the congruency of the different concepts and methods was tested to reveal the relationship of the Noccaea densiflora species complex. Nuclear ribosomal internal transcribed spacer, chloroplast trnL-F, and trnQ-50 rps16 regions were used for species delimitation using the multispecies coalescent model as implemented in two developed Bayesian methods. Internal transcribed spacer and trnL-F regions were also used for Templeton, Crandall, and Singh haplotype network analyses. In addition to morphological measurements from different populations and vouchers, specific bioclimatic data values were also used for the principal component analysis. Based on the analyses, it was determined that only one population of N. densiflora (Boiss. & Kotschy) F.K. Mey. and one of Noccaea microstyla (Boiss.) F.K. Mey. were clearly distinct, whereas the rest of the specimens remain taxonomically uncertain.