Research of the past few decades has revealed a great variability of metabolisms (e.g. adaptation to different microhabitats, feeding strategies, symbiosis, survival to stressful conditions) among benthic foraminiferal species. This metabolic variety is reflected in the cell by a great diversity of organelles, cellular organization and organelle associations. Despite the large number of publications examining the foraminiferal ultrastructure with transmission electron microscopy (TEM), only a fraction of the observed organelles have been identified. To gather all the knowledge about benthic foraminifera ultrastructure, an atlas based on existing literature and new observations of rotalid foraminifera was developed, as a part of a special issue entitled “Benthic Foraminiferal Ultrastructure Studies” (Marine Micropaleontology). Among other studies, this special issue provides a key to recognize the main organelles encountered in all examined benthic foraminiferal species, with known (e.g., nuclei, mitochondria, Golgi apparatus, endoplasmic reticulum, peroxisomes) or unknown functions (e.g., electron-opaque bodies, fibrillar vesicles). Cellular ultrastructure via TEM is a good way to obtain insights into physiology. Indeed, there are examples in the literature where ultrastructural observation led to hypotheses about foraminiferal metabolism, such as a specific distribution of mitochondria in response to hypoxia, vacuolization thought to play a role in denitrification, or endosymbionts providing an alternative metabolic pathway to their host. Another example of how TEM observations of the cell has proven a good tool to obtain insights into foraminiferal metabolism is kleptoplasty (i.e., the ability from some foraminiferal species to actively sequester chloroplasts stolen from microalgae within their endoplasm). Seven species of benthic foraminifera inhabiting photic zones were imaged using TEM to ascertain attributes of their kleptoplasts. Results show that there are differences in the way the investigated species organize their kleptoplasts within their endoplasm. This suggests behavioral strategies to expose and/or protect the kleptoplasts to/from light and/or to favor gas and/or nutrient exchange with their surrounding habitats. Also, different species had kleptoplasts in variable states of preservation/digestion, suggesting that some species are more efficient at kleptoplasty than others, as confirmed by complementary techniques.