We studied the occurrence, morphology and phenology of Dendroctonus micans in Lithuania and the fungi associated with the beetle at different developmental stages. The occurrence of D. micans was assessed in 19 seed orchards (at least 40 years old) of Picea abies (L. Karst.) situated in different parts of the country. Bark beetle phenology was studied in two sites: a seed orchard of P. abies and a plantation of Picea pungens (Engelm.). D. micans morphology was assessed under the dissection microscope using individuals at different developmental stages that were sampled during phenology observations. Communities of fungi associated with D. micans were studied using both fungal culturing methods and direct high-throughput sequencing from D. micans. Results showed that the incidence D. micans was relatively rare and D. micans was mainly detected in central and eastern Lithuania. The life cycle included the following stages: adult, egg, I–V developmental stage larvae and pupa. However, development of D. micans was quicker and its nests larger under the bark of P. pungens than of P. abies, indicating the effect of the host species. Fungal culturing and direct high-throughput sequencing revealed that D. micans associated fungi communities were species rich and dominated by yeasts from a class Saccharomycetes. In total, 319 fungal taxa were sequenced, among which Peterozyma toletana (37.5% of all fungal sequences), Yamadazyma scolyti (30.0%) and Kuraishia capsulate (17.7%) were the most common. Plant pathogens and blue stain fungi were also detected suggesting their potentially negative effects to both tree health and timber quality.