Abstract : Since it was discovered as the cause of Covid-19 infection, the SARS-CoV-2 Virus has continued to mutate. And the last is the discovery of the XBB.1.16 (Arcturus) subvariant in March 2023. In Indonesia, the spike in cases due to XBB.1.16 subvariant occurred in mid-April 2023 where the number of cases reached more than 1,000 per day. Phylogenetic analysis needs to be carried out to determine the evolution that has occurred in XBB subvariant in Indonesia, especially on Java Island, because Java Island is one of the most densely populated islands in Indonesia. The purpose of phylogenetic analysis is to determine the evolutionary relationship of SARS-CoV-2 in Java Island and to obtain information about pathogen through sequence data. This study aims to look at phylogenetic pattern of XBB subvariant SARS-CoV-2 in Covid-19 patients on Java Island. A total of 123 genome sequences of SARS-CoV-2 were taken from data available at GISAID from September 2022 to May 2023. The reference genome sequence of SARS-CoV-2 which was first discovered in Wuhan, China. Making phylogenetic patterns using Nextstrain Algorithm. Our data of the 123 whole genome sequences revealed 7 clades, namely Clade 22B, 22D, 22E, 22F, 21L, 23 A dan recombinant. A total of 27 Pango Lineages were identified. The dominant lineage were XBB.1.9.2, XBB.1.9.1 and XBB.1. There are also BQ lineages cocirculated with XBB lineages in Java Island. There are convergent evolution, of the spike protein that increase the binding affinity of SARS-CoV-2 S protein to human angiotensin-converting enzyme 2 (ACE 2) which is L452R, N460K and R346T. And also there are mutation that contribute to evasion of antiviral humoral immunity induced by vaccination and natural SARS-CoV-2 infection which is R346T, K444T and F486V. These mutations that causes faster spread and a higher infection rate than the previous variant were found in the XBB subvariant in Covid-19 patient in Java island. In Java island we can find that BQ lineages cocirculated with XBB lineages.