The Biosphere is considered to represent the Earth's crust, atmosphere, oceans, and ice caps and the living organisms that survive within this habitat. This paper considers the significance of comets and carbonaceous meteorites to the origin and evolution of the Biosphere and presents new Field Emission Scanning Electron Microscope (FESEM) images of indigenous microfossils in the Orgueil and Murchison meteorites. The discovery of microbial extremophiles in deep crustal rocks, hydrothermal vents and ancient ice has established that the biosphere is far more extensive than previously recognized. Chemical and molecular biomarkers and microfossils in Archaean rocks indicate that life appeared very early on the primitive Earth and the origin of the biosphere is closely linked with the emergence of life. The role of comets, carbonaceous meteorites, interstellar dust and asteroids in the delivery of water, organics and prebiotic chemicals to Earth during the Hadean (4.5–3.8 Ga) period of heavy bombardment has become more widely recognized. Spacecraft observations of the chemical compositions and characteristics of the nuclei of several comets (Halley, Borrelly, Wild 2, and Tempel 1) have established that comets contain complex organic chemicals; that water is the predominant volatile; and that high temperatures (~400 K) can be reached on the black (albedo~0.03) nuclei when near perihelion. The microscopic dust particles in the Tempel 1 ejecta are similar in size to the particulates of the Orgueil meteorite and evidence is mounting that comets may represent the parent bodies of the CI meteorites. Impact craters and pinnacles on comet Wild 2 suggest a thick crust. Episodic outbursts and jets of Halley, Borrelly, Wild 2 and Tempel 1 near perihelion indicate that localized regimes of liquid water may periodically exist beneath the thick crust of many comets. This increases the possibility that microbial life might survive in comets and therefore the widely accepted view that comets are devoid of liquid water and therefore sterile may be invalid. Consequently, the potential role of comets in the possible delivery of viable microorganisms, as well as water and organic chemicals, to Earth merits further consideration. FESEM investigations of CI and CM carbonaceous meteorites have resulted in the detection of well-preserved remains of large, complex and highly differentiated filamentous microfossils, mats, and consortia embedded in freshly fractured interior surfaces of the rock matrix. Energy Dispersive X-ray Spectroscopy (EDS) data indicate that these remains are mineralized and consequently they are interpreted to represent indigenous microfossils rather than recent microbial contaminants. The detection of indigenous microfossils in carbonaceous meteorites suggests that the paradigm of the endogenous origin of life on Earth may also require reconsideration.