Delimiting mobile genetic elements (MGEs) in bacterial genomes traditionally relies on experts in biology. This paper presents a process-oriented case-based reasoning (PO-CBR) approach to formalize and automate expert reasoning for MGE delimitation. In this study, expert knowledge is represented by process cases, where each case follows an ordered stepwise reasoning process based on genomic data on MGEs. These cases form adaptive computational workflows that can be applied to various types of bacterial strains and MGEs. A key feature of this approach is an adaptive mechanism that allows reasoning failures to trigger automatic adaptation rules. Tested on 254 manually annotated MGEs across 124 bacterial genomes, our approach successfully delimited 96.8% of these elements with high accuracy. This study demonstrates the feasibility of encoding biological expertise into a structured automated reasoning system that offers a reliable alternative to identify MGEs in bacterial genomes.