Coronavirus disease 2019 (COVID-19) emerged in December 2019 when the first case was reported in Wuhan, China, and turned into a pandemic. Whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a crucial role in understanding the disease. For this reason, we performed WGS of 101 SARS-CoV-2 strains obtained from individuals from two districts of Campania (Italy) from January to May 2021. The phylogenetic analysis of sequence data identified five types of clades including 10 different Pango lineages: 20A (Lineages B.1.258.17, B.1.258.14, and B.1.160) (n = 10; 9.9%), 20B (Lineages B.1.1.351 and B.1.374) (n = 5; 4.9%), 20E (EU1) (Lineages B.1.177.53, B.1.177.75, and B.1.177) (n = 5; 4.9%), 20I (Alpha.V1) (B.1.1.7) (n = 60; 59.4%), and 20J (Gamma.V3) (Lineage P.1.1) (n = 21; 20.7%). In the early time of the epidemic (January and February 2021), B.1.1.7 lineage was in 62% of samples only in Benevento district, while this lineage appears in Avellino later in 64% of samples from March to May. The occurrence of P.1.1 lineage spreading from March to the end of the study was recorded in all districts with the same frequencies of ~21%. The highest genomic distance was observed in Lineage P.1.1. Moreover, we identified 219 “known” missense mutations with different frequencies (114 in ORF1a/1b; 12 in ORF3a; 29 in S; 5 in M; 29 in N; and 5 each in ORF7a and ORF8). This report suggests the quickly spreading in Campania of new variants of SARS-CoV-2 and the strict surveillance of the occurrence of genetic variants of SARS-CoV-2.