Common spear rot (CSR) also known as crown disease (CD), is a disease known to affect young immature oil palm (Elaeis guineensis Jacq.) in the field. However, there is limited information on CSR disease incidences reported in Malaysia. Hence, this study was aimed to identify possible pathogens causing CSR disease on oil palm in Malaysia. Palm showing severe lesions and rotting of unopened spear leaves was identified, and the internal tissues from healthy and infected bole sections were sampled. Five fungal and 12 bacterial isolates were recovered from the infected tissues, while three fungal and two bacterial isolates were isolated from healthy tissue. Macroscopic identification of these cultures was conducted by observing the bacterial and fungal isolates grown in nutrient agar (NA) and potato dextrose agar (PDA), respectively. Molecular identification was carried out using internal transcribed spacer (ITS), translation elongation factor (TEF 1-α) and 16S primers through polymerase chain reaction (PCR). The identity of each isolate was determined using the BLASTN program through non-redundant database nucleotide collection. The sequence analysis showed most of the fungal isolates isolated were identical to Fusarium genus with 96.35% to 100.00% similarity when compared to sequences deposited in the GenBank. The species Fusarium solani was one of the most frequently recovered fungal isolates from the infected tissues. Meanwhile, one Erwinia sp., nine Klebsiella sp., three Dickeya sp. and one Enterococcus sp. were identified from the bacterial collection. Phylogenetic analysis revealed that all isolates of F. solani from the diseased palm clustered together with F. solani belonging to other hosts, validating the identity of the isolates. Apart from that, Klebsiella sp. was also isolated and could also be responsible for causing CSR but requires further validation through Koch’s postulate assessment. Nevertheless, this is the first study reporting the isolation of Klebsiella sp. in diseased CSR oil palm.