<p><strong>Background</strong>: Secondary metabolites are important chemomarkers. However, as a system to confront biotic and abiotic stress, chemical composition can vary, improving the phenotypic plasticity of plants. We determined the potential of the foliar and floral phenolic composition, floral carotenoid contents to discriminate between two subspecies of <em>Fouquieria splendens</em> and assessed the effect of atypical environmental conditions on the chemical composition of a relict population of the subspecies <em>splendens</em>.</p><p><strong>Hypothesis</strong>: We hypothesized that chemical differences have arisen between the analyzed subspecies and in the relict population allowing the differentiation between them.</p><p><strong>Species studied: </strong><em>Fouquieria splendens</em> subsp. <em>splendens </em>and<em> Fouquieria splendens</em> subsp. <em>campanulata </em>(Fouquieriaceae).</p><p><strong>Study site and years of study: </strong>Mezquital, Peñón Blanco, and San Juan del Río, Durango, México. March to August 2016.<strong></strong></p><p><strong>Methods</strong>: Foliar and floral extracts were analyzed by HPLC-DAD, UV-visible spectrophotometry, and FTIR-ATR. Multivariate analysis was used to assess the sample distinctiveness and to establish the relation between the chemical composition and environmental variables.<em></em></p><p><strong>Results</strong>:<em> </em>The chemical composition was highly conserved between the analyzed samples. Contrarily, an evident distinctiveness between phytochemical contents was observed. Soil parameters were the factors determining the particular quantitative phenolic profiles.<strong></strong></p><p><strong>Conclusions:</strong><em> </em>The analyzed subspecies and populations showed similar chemical patterns; however, quantitative variations, determined by soil texture, electrical conductivity, organic matter, organic carbon, and contents of K, Ca, and Na, allowed to differentiate them. The important phenolic quantitative variation of the atypical population of <em>F. splendens</em> subsp. <em>splendens</em> suggests a relevant contribution of phenolic compounds to the adaptation to its relict condition.</p>