An underwater serial sectioning tomography technique is shown capable of determining three-dimensional Chlorophyll a (Chl a) microstructure in phytoplankton distributions. The technique involves scanning a 457-nm illumination plane through a range of distances parallel to the imaging plane of a digital CCD camera. Images of induced fluorescence at 685 nm in the sequentially illuminated plane are recorded. A theoretical model of the imaging process in the form of i=ln c+Ac+x shows that the image i is a function of a spatially varying c (Chl a) dependent absorption component A and a spatially invariant attenuation component x. A numerical inverse method, incorporating an environmentally dependent calibration constant, is used to calculate Chl a values from the image intensities for three-dimensional presentation. A stable reconstruction, not affected by noise-induced error propagation, is demonstrated. Laboratory testing of a prototype system has shown that Chl a concentrations from 0.1 to 2.0 mg Chl a m-3 at a 0.1 mg Chl a m-3 resolution can be determined. The limiting factor in the imaging process is the rapid attenuation of the fluoresced 685-nm light which determines the system optical depth &xgr;. With 0.1 mg Chl a m-3 as a minimum, &xgr;=0.97. At this &xgr; and c(685)≤0.7 m-1, a 1 m3 volume of 0.1 mg Chl a m-3 can be imaged with a spatial resolution of 1 cm3. At higher Chl a levels, larger values of &xgr; permit larger volumes to be imaged. The remote sensing aspect of this underwater tomography technique permits in situ Chl a microstructure information to be obtained without disturbing the naturally occurring phytoplankton distributions, thus providing a new mechanism for microscale biological and physical oceanographic investigation. ¿ American Geophysical Union 1995