Bacillus is a highly diverse genus that can be problematic in both industrial and medical settings due to their intrinsic antibiotic resistance and production of endospores, which makes them highly resistant to extreme conditions. Bacteriophages have the potential to serve as a viable alternative to antimicrobial compounds as they cause rapid lysis of bacteria for their own proliferation. In this study, two bacteriophages, PumA1 and PumA2 were isolated from soil, sequenced, and genetically characterised. Sequence analysis identified the two phages as novel, however they share protein homologies to the phi29-like phage group, relating back to the type phage, phi29. Genome arrangements of PumA1 and PumA2 also share the same modular pattern and features. A whole genome comparison was undertaken using pairwise nucleotide identities, gene content analysis and both reticulate network and traditional linear phylogenetic approaches. This analysis shows that the phi29-like phages should be classified into seven clusters and four singleton phages not clustered. The reticulate network confirmed that the phi29-like phages are highly conserved and share few proteins with other phages in the global network. PumA1 and PumA2 share high genetic mosaicism to each other as well as another phage WhyPhy, isolated in the USA and formed their own cluster. This cluster are the only phi29-like phages recorded to infect B. pumilus and this led to an investigation of their host receptor sites. Sequence analysis of phage resistant colonies revealed mutations in the tagT and tagF genes. These genes are a part of the wall teichoic acid synthesis operons and form the receptor site for the PumA1 and PumA2. Understanding phage evolution using both traditional phylogenetic approaches and reticulate network models will ultimately help uncover evolutionary relationships between phage groups. This knowledge is invaluable as phages start to become legitimate treatment options in both human health and industrial sterilisation processes.