Coastal reef degradation and widespread bleaching of corals, i.e. loss of p
igments and/or symbiotic zooxanthellae, is increasing globally. Remote sens
ing from boats, aircraft or satellites has great potential for assessing th
e extent of reef change, but will require ground-verified spectral algorith
ms characteristic of healthy and degraded reef populations. We collected se
ven species of Caribbean reef corals and also representative macroalgae fro
m reefs near Lee Stocking Island, Bahamas and quantified their pigments usi
ng high performance liquid chromatography. We also measured the fluorescenc
e and reflectance spectra of corals and macroalgae using an in situ benthic
spectrofluorometer. In visibly pigmented (unbleached) coral from 4 to 5 m
depth, the mean (+/- SD) surface density of pigments (3.0 +/- 1.3 mu g chlo
rophyll-a cm(-2) and 2.1 +/- 0.7 mu g peridinin cm(-2)) was similar between
colonies of the same species, but differed among species. The mean quantit
y of pigment per zooxanthella(1.8 +/- 0.9 pg chi-a cell(-1) and 1.4 +/- 0.7
pg peridinin cell(-1)) also differed among species and sometimes between c
olonies of the same species. Chi-a and peridinin densities per surface area
of coral were positively correlated. When excited with blue light (480 nm)
, macroalgae and corals had typical chlorophyll fluorescence with a peak at
680 nm and a smaller shoulder peak at 730 to 740 nm. Most corals, unlike m
acroalgae, also had distinct fluorescence peaks between 500 and 530 nm. In
visibly bleached corals 680 nm fluorescence was greatly reduced in amplitud
e. Pigmented coral, under natural lighting conditions, had a reflected ligh
t peak at about 570 nm. Reflectance increased over all wavelengths in bleac
hed corals, with the greatest increase at the wavelengths where chlorophyll
and accessory pigments absorb light, i.e. 670 and 450 to 550 nm. Both fluo
rescence and reflectance spectra appear promising to remotely differentiate
between pigmented and bleached coral and between coral and macroalgae.