<p>Chlorophylls and carotenoids constitute the predominant plant pigments, playing pivotal roles in photosynthesis, pollinator attraction, and defense against biotic and abiotic stress. However, differences in pigment composition between floral and vegetative organs, along with their functional coordination, remain poorly understood. We quantified chlorophyll (chlorophyll a, chlorophyll b and total chlorophyll) and total carotenoid contents in flower organs (petals, sepals and floral lips), roots, stems and leaves across 36 <i>Dendrobium</i> species. The results revealed significantly higher variation in pigment contents of flowers, particularly petal total carotenoids, compared to conserved vegetative pigment patterns. Leaves exhibited the highest chlorophyll, whereas floral lips contained the highest total carotenoid content. Ancestral state reconstruction further supported strong phylogenetic conservatism in vegetative pigment traits and marked evolutionary lability in floral pigment traits. Strong positive correlations were observed among pigments of flowers (petals, sepals, floral lips), in contrast to the non-significant correlations between pigment contents of flowers and vegetative organs. Among vegetative organs, leaf pigment levels were positively correlated with stem pigment levels, but with root pigment levels. Based on principal component analysis (PCA), the first axis of multivariate variation was primarily defined by floral chlorophylls and total carotenoids, whereas the second axis represented variability derived from pigment profiles of vegetative organ. Floral and vegetative pigments exhibited clear evolutionary and functional decoupling, a pattern robust to phylogenetic correction. These findings demonstrate distinct evolutionary trajectories of floral versus vegetative pigmentation, reflecting functional specialization and modular regulatory mechanisms in <i>Dendrobium</i>.</p>