The scientific petroleum community now recognizes that island- and archipelago-type molecules coexist in the asphaltene fraction of crude oils and that their relative abundance depends on sample origin. This fact means that geologic factors such as the kerogen type, source rock lithology, thermal maturity, and secondary alteration processes in the reservoir are expected to control the proportions of these asphaltene architectures, in a first stage; however, the influence of these factors is not well understood. In this work, we combined biomarker analyses, spectroscopic characterization, and the p-nitrophenol fractionation method to confirm the coexistence of island- and archipelago-type molecules in the asphaltenes of a marine crude oil family originating from a carbonate source rock containing type II kerogen. The effects of thermal maturity, hydrocarbon generation, and crude oil biodegradation on the distribution, structure, and aggregation behaviors of island and archipelago asphaltenes obtained as the A1 and A2 subfractions were also studied. The results indicated that at the early mature stage, the generated immature crude oils show very similar proportions of island to archipelago structures inherited from the parent kerogen; then, thermal maturity and the combination of hydrocarbon charges emitted by the source rock at different events alter this relationship through an increase in the island components. Biodegradation was found to cause insignificant changes in either the relative abundance of island and archipelago asphaltenes or in their structural features. The increase in maturity also produced the progressive aromatization of both island and archipelago components, accompanied by the presence of large and very large asphaltene aggregates possibly formed with the participation of metalloporphyrins. These findings provide new insights into asphaltene geochemistry and chemistry to understand the effects of sample origin on the coexistence of island and archipelago structures, the chemical transformation pathways adopted by each of these molecular architectures under natural thermal conditions, and the modification of their aggregation behavior.