Flower colour is mainly due to the accumulation of flavonoids, carotenoids and betalains in the petals. Of these pigments, flavonoids are responsible for a wide variety of colours ranging from pale yellow (flavones, flavonols and flavanodiols) to blue-violet (anthocyanins). This character plays a crucial ecological role by attracting and guiding pollinators. Moreover, in the ornamental plants market, colour has been consistently identified as the main feature chosen by consumers when buying flowers. Considering the importance of this character, the aim of this study was to evaluate flower colour in the native Chilean geophyte Alstroemeria pallida, by using three different approaches. Firstly, the phenotype was assessed using both a colour chart and a colourimeter, obtaining CIELab parameters. Secondly, the anthocyanin content of the pigmented tepals was evaluated by high-performance liquid chromatography (HPLC), and finally, the expression of two key flavonoid genes, chalcone synthase (CHS) and anthocyanidin synthase (ANS) was analysed using real-time polymerase chain reaction (PCR). Visual evaluation of A. pallida flower colour identified 5 accessions, ranging from white (Royal Horticultural Society (RHS) N999D) to pink (RHS 68C). Moreover, this visual evaluation of the accessions correlated highly with the CIELab parameters obtained by colourimetry. An anthocyanidin corresponding to a putative 6-hydroxycyanidin was identified, which was least abundant in the white accession (RHS N999D). Although CHS was not expressed differentially between the accessions, the expression of ANS was significantly higher in the accession with pink flowers (RHS 68C). These results suggest a correlation between phenotype, anthocyanin content and ANS expression for determining flower colour of A. pallida, which could be of interest for further studies, especially those related to the breeding of this species with ornamental value.