A chromophore is the part of a molecule responsible for its color.  The color arises when a molecule absorbs certain wavelengths of visible light and transmits or reflects others. The chromophore is a region in the molecule where the energy difference between two different molecular orbitals falls within the range of the visible spectrum. Visible light that hits the chromophore can thus be absorbed by exciting an electron from its ground state into an excited state.
Conjugated pi-bond system chromophores 
In the conjugated chromophores, the electrons jump between energy levels that are extended pi orbitals, created by a series of alternating single and double bonds, often in aromatic systems. Common examples include retinal (used in the eye to detect light), various food colorings, fabric dyes (azo compounds), pH indicators, lycopene, β-carotene, and anthocyanins. Various factors in a chromophore's structure go into determining at what wavelength region in a spectrum the chromophore will absorb. Lengthening or extending a conjugated system with more unsaturated (multiple) bonds in a molecule will tend to shift absorption to longer wavelengths. Woodward-Fieser rules can be used to approximate ultraviolet-visible maximum absorption wavelength in organic compounds with conjugated pi-bond systems.
Some of these are metal complex chromophores, which contain a metal in a coordination complex with ligands. Examples are chlorophyll (used by plants for photosynthesis) and hemoglobin (the oxygen transporter in the blood of vertebrate animals). In these two examples, a metal is complexed at the center of a porphyrin ring: the metal being iron in the heme group of hemoglobin, or magnesium in the case of chlorophyll. The highly conjugated pi-bonding system of the porphyrin ring absorbs visible light. The nature of the central metal can also influence the absorption spectrum of the metalloporphyrin complex or properties such as excited state lifetime.
An auxochrome is a functional group of atoms attached to the chromophore which modifies the ability of the chromophore to absorb light, altering the wavelength or intensity of the absorption.
Halochromism in chromophores 
Halochromism occurs when a substance changes color as the pH changes. This is a property of pH indicators, whose molecular structure changes upon certain changes in the surrounding pH. This change in structure affects a chromophore in the pH indicator molecule. For example, phenolphthalein is a pH indicator whose structure changes as pH changes as shown in the following table:
|Conditions||acidic or near-neutral||basic|
||pink to fuchsia|
In a pH range of about 0-8, the molecule has three aromatic rings all bonded to a tetrahedral sp3 hybridized carbon atom in the middle which does not make the π-bonding in the aromatic rings conjugate. Because of their limited extent, the aromatic rings only absorb light in the ultraviolet region, and so the compound appears colorless in the 0-8 pH range. However as the pH increases beyond 8.2, that central carbon becomes part of a double bond becoming sp2 hybridized and leaving a p orbital to overlap with the π-bonding in the rings. This makes the three rings conjugate together to form an extended chromophore absorbing longer wavelength visible light to show a fuchsia color. At pH ranges outside 0-12, other molecular structure changes result in other color changes; see Phenolphthalein for details.
See also 
- Causes of Color: physical mechanisms by which color is generated.
- High Speed Nano-Sized Electronics May be Possible with Chromophores - Azonano.com
- IUPAC Gold Book Chromophore
- Gouterman, M. (1978) Optical spectra and electronic structure of porphyrins and related rings. In Dolphin, D. (ed.) The porphyrins. Academic Press, New York. Volume III, Part A, pp 1-165
- Scheer, H. (2006) An overview of chlorophylls and bacteriochlorophylls: biochemistry, biophysics, functions and applications. Advances in Photosynthesis and Respiration, vol 25, pp 1-26
- Shapley, P. (2012) Absorbing light with organic molecules. http://butane.chem.uiuc.edu/pshapley/GenChem2/B2/1.html
- UV-Visible Absorption Spectra