The major difference is that they have completely different cellular makeup.. Bacteria are said to be prokaryotic organisms, meaning they do not possess nucleus while fungi are eukaryotic organisms in which they have well-defined nucleus. Additionally, bacteria are considered unicellular microorganisms which can only be seen under a microscope whereas fungi are more complex microorganisms except for yeast. Both organisms have cell walls but the components within the cell walls are different. Most fungi are composed of networks of long hollow tubes called hyphae. Each hypha is bordered by a rigid wall usually made of chitin—the same material that forms the exoskeletons of insects. Hyphae grow by elongation at the tips and by branching to form a dense network called mycelium. As the mycelium grows, it produces huge fruiting bodies and other structures which contain reproductive spores. In contrast, the key component of the bacterial cell wall is called peptidoglycan. The bacterial cell also has a cell membrane containing cytoplasm.