“DNA barcoding” therefore accepts that species limits are established   following traditional practices of taxonomy, usually based on morphology, and   the DNA information is fitted into this system of predefined taxonomic   groups. This approach is problematic because the correspondence of sequence   variation with existing Linnean binomials is expected to be inexact. This may   be because of the existence of unrecognized cryptic species (Hebert et al., 2004a, 2004b)   or incongruence of gene histories confounding species recognition (Funk and Omland, 2003; Meyer   and Paulay, 2005; Monaghan et al., 2006) or because procedures for   species delimitation of the traditional taxonomy have been vague or species   concepts have been applied inconsistently (Agapow et al., 2004; Cracraft, 1992; Meyer and Paulay,   2005; Wiens and Penkrot, 2002). To avoid these problems, a DNA-based   taxonomic system should use the sequence information itself as the primary   information source for establishing group membership and defining species   boundaries.

因此，“DNA条形码”承认的物种界限是按照传统的分类方法建立的，通常是基于形态学的，并且DNA信息被要求适配到这个预先定义的分类群系统中。这种方法是有问题的，因为序列变异与现有的林奈双名系统的对应关系是不准确的。这可能是因为存在无法辨识的隐存种（Hebert et al.,   2004a, 2004b），或者不同基因的历史不一致，混淆了物种识别（Funk and Omland,   2003; Meyer and Paulay, 2005; Monaghan et al., 2006），或者是因为传统分类法的物种定界程序一直都比较模糊，或者物种概念的应用不一致（Agapow et al.,   2004; Cracraft, 1992; Meyer and Paulay, 2005; Wiens and Penkrot, 2002）。为了避免这些问题，基于DNA的分类系统应该使用序列信息本身作为建立群体成员和定义物种边界的主要信息源。